Nietert, Manuel Manfred

[["dc.bibliographiccitation.journal","Oncology Research and Treatment"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Ruehlmann, Felix"],["dc.contributor.author","Nietert, Manuel M."],["dc.contributor.author","Sprenger, Thilo"],["dc.contributor.author","Wolff, Hendrik Andreas"],["dc.contributor.author","Homayounfar, Kia"],["dc.contributor.author","Ghadimi, Michael B."],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Liersch, Torsten"],["dc.contributor.author","Conradi, Lena-Christin"],["dc.date.accessioned","2018-11-07T09:34:12Z"],["dc.date.available","2018-11-07T09:34:12Z"],["dc.date.issued","2014"],["dc.identifier.isi","000343816900255"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32127"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Karger"],["dc.publisher.place","Basel"],["dc.title","SRC expression in locally advanced rectal cancer-before and after neoadjuvant chemoradiotherapy"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1072"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","Journal of Personalized Medicine"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Vinhoven, Liza"],["dc.contributor.author","Voskamp, Malte"],["dc.contributor.author","Nietert, Manuel Manfred"],["dc.date.accessioned","2022-01-11T14:07:52Z"],["dc.date.available","2022-01-11T14:07:52Z"],["dc.date.issued","2021"],["dc.description.abstract","The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA’s own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online."],["dc.description.abstract","The MINERVA platform is currently the most widely used platform for visualizing and providing access to disease maps. Disease maps are systems biological maps of molecular interactions relevant in a certain disease context, where they can be used to support drug discovery. For this purpose, we extended MINERVA’s own drug and chemical search using the MINERVA plugin starter kit. We developed a plugin to provide a linkage between disease maps in MINERVA and application-specific databases of candidate therapeutics. The plugin has three main functionalities; one shows all the targets of all the compounds in the database, the second is a compound-based search to highlight targets of specific compounds, and the third can be used to find compounds that affect a certain target. As a use case, we applied the plugin to link a disease map and compound database we previously established in the context of cystic fibrosis and, herein, point out possible issues and difficulties. The plugin is publicly available on GitLab; the use-case application to cystic fibrosis, connecting disease maps and the compound database CandActCFTR, is available online."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.3390/jpm11111072"],["dc.identifier.pii","jpm11111072"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/97883"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-507"],["dc.relation.eissn","2075-4426"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Mapping Compound Databases to Disease Maps—A MINERVA Plugin for CandActBase"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1278"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Biomolecules"],["dc.bibliographiccitation.volume","12"],["dc.contributor.affiliation","Voskamp, Malte; 1Department of Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, 37077 Göttingen, Germany"],["dc.contributor.affiliation","Vinhoven, Liza; 1Department of Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, 37077 Göttingen, Germany"],["dc.contributor.affiliation","Stanke, Frauke; 2Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany"],["dc.contributor.affiliation","Hafkemeyer, Sylvia; 4Mukoviszidose Institut gGmbH, In den Dauen 6, 53117 Bonn, Germany"],["dc.contributor.affiliation","Nietert, Manuel Manfred; 1Department of Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, 37077 Göttingen, Germany"],["dc.contributor.author","Voskamp, Malte"],["dc.contributor.author","Vinhoven, Liza"],["dc.contributor.author","Stanke, Frauke"],["dc.contributor.author","Hafkemeyer, Sylvia"],["dc.contributor.author","Nietert, Manuel Manfred"],["dc.contributor.editor","Song, Jiangning"],["dc.date.accessioned","2022-10-04T10:21:49Z"],["dc.date.available","2022-10-04T10:21:49Z"],["dc.date.issued","2022"],["dc.date.updated","2022-11-11T13:13:13Z"],["dc.description.abstract","An adequate visualization form is required to gain an overview and ultimately understand the complex and diverse biological mechanisms of diseases. Recently, disease maps have been introduced for this purpose. A disease map is defined as a systems biological map or model that combines metabolic, signaling, and physiological pathways to create a comprehensive overview of known disease mechanisms. With the increase in publications describing biological interactions, efforts in creating and curating comprehensive disease maps is growing accordingly. Therefore, new computational approaches are needed to reduce the time that manual curation takes. Test mining algorithms can be used to analyse the natural language of scientific publications. These types of algorithms can take humanly readable text passages and convert them into a more ordered, machine-usable data structure. To support the creation of disease maps by text mining, we developed an interactive, user-friendly disease map viewer. The disease map viewer displays text mining results in a systems biology map, where the user can review them and either validate or reject identified interactions. Ultimately, the viewer brings together the time-saving advantages of text mining with the accuracy of manual data curation."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2022"],["dc.identifier.doi","10.3390/biom12091278"],["dc.identifier.pii","biom12091278"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/114511"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-600"],["dc.publisher","MDPI"],["dc.relation.eissn","2218-273X"],["dc.rights","CC BY-SA 4.0"],["dc.title","Integrating Text Mining into the Curation of Disease Maps"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Onkologie"],["dc.bibliographiccitation.volume","36"],["dc.contributor.author","Conradi, Lena-Christin"],["dc.contributor.author","Quack, H."],["dc.contributor.author","Sprenger, Thilo"],["dc.contributor.author","Wolff, Hendrik Andreas"],["dc.contributor.author","Binder, L."],["dc.contributor.author","Ghadimi, Michael B."],["dc.contributor.author","Homayounfar, Kia"],["dc.contributor.author","Bleckmann, Annalen"],["dc.contributor.author","Lorenzen, Stephan"],["dc.contributor.author","Nietert, Manuel M."],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Liersch, Torsten"],["dc.date.accessioned","2018-11-07T09:19:02Z"],["dc.date.available","2018-11-07T09:19:02Z"],["dc.date.issued","2013"],["dc.format.extent","73"],["dc.identifier.isi","000326360900167"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/28546"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Karger"],["dc.publisher.place","Basel"],["dc.relation.issn","1423-0240"],["dc.relation.issn","0378-584X"],["dc.title","5-FU dose monitoring under neoadjuvant radiochemotherapy and adjuvant chemotherapy for locally advanced rectal cancer"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","12351"],["dc.bibliographiccitation.firstpage","12351"],["dc.bibliographiccitation.issue","20"],["dc.bibliographiccitation.journal","International Journal of Molecular Sciences"],["dc.bibliographiccitation.volume","23"],["dc.contributor.affiliation","Vinhoven, Liza; 1Department of Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, 37077 Göttingen, Germany"],["dc.contributor.affiliation","Stanke, Frauke; 2Clinic for Pediatric Pneumology, Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625 Hannover, Germany"],["dc.contributor.affiliation","Hafkemeyer, Sylvia; 4Mukoviszidose Institut, In den Dauen 6, 53117 Bonn, Germany"],["dc.contributor.affiliation","Nietert, Manuel Manfred; 1Department of Medical Bioinformatics, University Medical Center Göttingen, Goldschmidtstraße 1, 37077 Göttingen, Germany"],["dc.contributor.author","Vinhoven, Liza"],["dc.contributor.author","Stanke, Frauke"],["dc.contributor.author","Hafkemeyer, Sylvia"],["dc.contributor.author","Nietert, Manuel Manfred"],["dc.contributor.editor","Guerrini, Gabriella"],["dc.contributor.editor","Giovannoni, Maria P."],["dc.date.accessioned","2022-12-01T08:31:41Z"],["dc.date.available","2022-12-01T08:31:41Z"],["dc.date.issued","2022"],["dc.date.updated","2022-11-11T13:12:17Z"],["dc.description.abstract","Cystic fibrosis is a genetic disease caused by mutation of the CFTR gene, which encodes a chloride and bicarbonate transporter in epithelial cells. Due to the vast range of geno- and phenotypes, it is difficult to find causative treatments; however, small-molecule therapeutics have been clinically approved in the last decade. Still, the search for novel therapeutics is ongoing, and thousands of compounds are being tested in different assays, often leaving their mechanism of action unknown. Here, we bring together a CFTR-specific compound database (CandActCFTR) and systems biology model (CFTR Lifecycle Map) to identify the targets of the most promising compounds. We use a dual inverse screening approach, where we employ target- and ligand-based methods to suggest targets of 309 active compounds in the database amongst 90 protein targets from the systems biology model. Overall, we identified 1038 potential target–compound pairings and were able to suggest targets for all 309 active compounds in the database."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft DFG"],["dc.identifier.doi","10.3390/ijms232012351"],["dc.identifier.pii","ijms232012351"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/118235"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-621"],["dc.publisher","MDPI"],["dc.relation.eissn","1422-0067"],["dc.relation.isreplacedby","hdl:2/118235"],["dc.rights","Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)."],["dc.title","Complementary Dual Approach for In Silico Target Identification of Potential Pharmaceutical Compounds in Cystic Fibrosis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.contributor.author","Islam, Shariful"],["dc.contributor.author","Nietert, Manuel Manfred"],["dc.contributor.author","Haberl, Michael"],["dc.contributor.author","Friede, Tim"],["dc.contributor.author","Beißbarth, Tim"],["dc.date.accessioned","2020-03-27T12:32:56Z"],["dc.date.available","2020-03-27T12:32:56Z"],["dc.date.issued","2015"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/63385"],["dc.notes.preprint","yes"],["dc.relation.conference","Computational Models in Biology and Medicine"],["dc.relation.eventlocation","Leipzig"],["dc.relation.eventstart","2015-09"],["dc.relation.iserratumof","yes"],["dc.title","Automated characterization of cell tracks and classification by using their position coordinates and velocity components"],["dc.type","conference_paper"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Cancer"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Bleckmann, Annalen"],["dc.contributor.author","Kirchner, Benjamin"],["dc.contributor.author","Nietert, Manuel"],["dc.contributor.author","Peeck, Micha"],["dc.contributor.author","Balkenhol, Marko"],["dc.contributor.author","Egert, Daniela"],["dc.contributor.author","Rohde, T. Veit"],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Pukrop, Tobias"],["dc.date.accessioned","2021-04-14T08:31:20Z"],["dc.date.available","2021-04-14T08:31:20Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1186/s12885-020-07459-z"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/83564"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.relation.eissn","1471-2407"],["dc.title","Impact of pre-OP independence in patients with limited brain metastases on long-term survival"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1463"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","International Journal of Colorectal Disease"],["dc.bibliographiccitation.lastpage","1469"],["dc.bibliographiccitation.volume","32"],["dc.contributor.author","Lowes, Markus"],["dc.contributor.author","Kleiss, Mathias"],["dc.contributor.author","Lueck, Rainer"],["dc.contributor.author","Detken, Sven"],["dc.contributor.author","König, Alexander Otto"],["dc.contributor.author","Nietert, Manuel M."],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Stanek, Kathrin"],["dc.contributor.author","Langer, Claus"],["dc.contributor.author","Ghadimi, Michael B."],["dc.contributor.author","Conradi, Lena-Christin"],["dc.contributor.author","Homayounfar, Kia"],["dc.date.accessioned","2019-07-09T11:44:24Z"],["dc.date.available","2019-07-09T11:44:24Z"],["dc.date.issued","2017"],["dc.description.abstract","PURPOSE: Multidisciplinary tumor boards (MDT) have been advocated as standard of care in modern oncology. German guidelines for metastasized colorectal cancer (mCRC) recommend MDT discussion of colon cancer patients after completion of primary tumor therapy but stage IV colon cancer as well as rectal cancer patients prior to any therapy. In this health care research study, we evaluated application and decisional consequences of this approach in clinical routine. METHODS: All major institutions providing oncological care in southern Lower Saxony and Northern Hesse (N = 11) were invited. Patients with mCRC diagnosed between 01/2011 and 12/2013 were eligible. Data were collected using a standardized patient report form and stored in a GCP-conform EDC-system (secuTrial®). RESULTS: A university medical center, four teaching hospitals, one communal hospital, and three oncological focus practices participated in the study. In total, 470 patients with a median age of 70 years were enrolled. Guideline conform MDT discussion was performed in 63% of operated colon cancer patients, 38% of stage IV colon cancer patients and 47% of rectal cancer patients, respectively. Resection of metastases was performed in 41% of cases. Patients ≥70 years (n = 250) received significantly more often treatment following MDT discussion (86 versus 64%, p = 0.0002). Not the resection rate (48 versus 57%, p = 0.1574) but indication for preoperative chemotherapy (57 versus 33%, p = 0.0056) significantly differed when patients with single organ metastases experienced MDT discussion. CONCLUSIONS: MDT discussion is not as established as advocated by national guidelines. Treatment decisions differ especially in older patients and those with single organ metastases."],["dc.identifier.doi","10.1007/s00384-017-2871-z"],["dc.identifier.pmid","28779354"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14738"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/59003"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","The utilization of multidisciplinary tumor boards (MDT) in clinical routine: results of a health care research study focusing on patients with metastasized colorectal cancer"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","522"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","American Journal of Surgical Pathology"],["dc.bibliographiccitation.lastpage","531"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Conradi, Lena-Christin"],["dc.contributor.author","Styczen, Hanna"],["dc.contributor.author","Sprenger, Thilo"],["dc.contributor.author","Wolff, Hendrik Andreas"],["dc.contributor.author","Roedel, Claus"],["dc.contributor.author","Nietert, Manuel M."],["dc.contributor.author","Homayounfar, Kia"],["dc.contributor.author","Gaedcke, Jochen"],["dc.contributor.author","Kitz, Julia"],["dc.contributor.author","Talaulicar, Recca"],["dc.contributor.author","Becker, Heinz"],["dc.contributor.author","Ghadimi, Michael B."],["dc.contributor.author","Middel, Peter"],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Rüschoff, Josef R."],["dc.contributor.author","Liersch, Torsten"],["dc.date.accessioned","2018-11-07T09:26:46Z"],["dc.date.available","2018-11-07T09:26:46Z"],["dc.date.issued","2013"],["dc.description.abstract","In patients with advanced rectal cancer (cUICC II and III) multimodality therapy resulted in better long-term local tumor control. Ongoing clinical trials are focusing on therapy intensification to improve disease-free (DFS) and cancer-specific survival (CSS), the integration of biomarkers for prediction of individual recurrence risk, and the identification of new targets. In this context, we investigated HER-2, a member of the epidermal growth factor receptor family, whose expression pattern and role was unclear in rectal cancer. A total of 264 patients (192 male, 72 female; median age 64 y) received standardized multidisciplinary treatment according to protocols of phase II/III trials of the German Rectal Cancer Study Group. HER-2 status was determined in pretherapeutic biopsies and resection specimens using immunohistochemistry scoring and detection of silver in situ hybridization amplification. Tumors with an immunohistochemistry score of 3(+) or silver in situ hybridization ratios of >= 2.0 were classified HER-2 positive; these results were correlated with clinicopathologic parameters [eg, resection (R) status, nodal status ((y)pN)], DFS, and CSS. Positive HER-2 status was found in 12.4% of biopsies and in 26.7% of resected specimens. With a median follow-up of 46.5 months, patients with HER-2 positivity showed in trend a better DFS (P = 0.1) and a benefit in CSS (P = 0.03). The 5-year survival rate was 96.0% (HER-2 positive) versus 80.0% (HER-2 negative). In univariate and multivariate analyses, HER-2 was an independent predictor for CSS (0.02) along with the (y)pN status (P < 0.00001) and R status (P = 0.011). HER-2 amplification is detectable in a relevant proportion (26.7%) of rectal cancer patients. For the development of innovative new therapies, HER-2 may represent a promising target and should be further assessed within prospective clinical trials."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [KFO 179-2]"],["dc.identifier.doi","10.1097/PAS.0b013e318272ff4d"],["dc.identifier.isi","000316184000006"],["dc.identifier.pmid","23282976"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/30374"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Lippincott Williams & Wilkins"],["dc.relation.issn","1532-0979"],["dc.relation.issn","0147-5185"],["dc.title","Frequency of HER-2 Positivity in Rectal Cancer and Prognosis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Oncology Research and Treatment"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Quack, H."],["dc.contributor.author","Stanek, K."],["dc.contributor.author","Wolff, Hendrik Andreas"],["dc.contributor.author","Dröge, Leif Hendrik"],["dc.contributor.author","Binder, L."],["dc.contributor.author","Bleckmann, Annalen"],["dc.contributor.author","Nietert, Manuel M."],["dc.contributor.author","Beißbarth, Tim"],["dc.contributor.author","Lorenzen, Stephan"],["dc.contributor.author","Liersch, Torsten"],["dc.contributor.author","Ghadimi, Michael B."],["dc.contributor.author","Conradi, Lena-Christin"],["dc.date.accessioned","2018-11-07T09:34:11Z"],["dc.date.available","2018-11-07T09:34:11Z"],["dc.date.issued","2014"],["dc.format.extent","83"],["dc.identifier.isi","000343816900196"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/32125"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Karger"],["dc.publisher.place","Basel"],["dc.relation.issn","2296-5262"],["dc.relation.issn","2296-5270"],["dc.title","Effects of 5-FU dose monitoring under neoadjuvant radiochemotherapy for locally advanced rectal cancer"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]