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Article ; Online: Human variation databases.

Küntzer, Jan / Eggle, Daniela / Klostermann, Stefan / Burtscher, Helmut

Database : the journal of biological databases and curation

2010 Volume 2010, Page(s) baq015

Abstract: More than 100,000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific ... ...

Abstract	More than 100,000 human genetic variations have been described in various genes that are associated with a wide variety of diseases. Such data provides invaluable information for both clinical medicine and basic science. A number of locus-specific databases have been developed to exploit this huge amount of data. However, the scope, format and content of these databases differ strongly and as no standard for variation databases has yet been adopted, the way data is presented varies enormously. This review aims to give an overview of current resources for human variation data in public and commercial resources.
MeSH term(s)	DNA Mutational Analysis ; Databases, Genetic/standards ; Disease/genetics ; Genetic Variation ; Germ-Line Mutation ; Humans ; Mutation ; Neoplasms/genetics ; Polymorphism, Single Nucleotide
Language	English
Publishing date	2010-07-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2496706-3
ISSN	1758-0463 ; 1758-0463
ISSN (online)	1758-0463
ISSN	1758-0463
DOI	10.1093/database/baq015
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Mining gene-centric relationships from literature: the roles of gene mutation and gene expression in supporting drug discovery.

Tari, Luis / Patel, Jagruti / Küntzer, Jan / Li, Ying / Peng, Zhengwei / Wang, Yuan / Aguiar, Laura / Cai, James

International journal of data mining and bioinformatics

2015 Volume 10, Issue 4, Page(s) 357–373

Abstract: Identifying drug target candidates is an important task for early development throughout the drug discovery process. This process is supported by the development of new high-throughput technologies that enable better understanding of disease mechanism. ... ...

Abstract	Identifying drug target candidates is an important task for early development throughout the drug discovery process. This process is supported by the development of new high-throughput technologies that enable better understanding of disease mechanism. It becomes critical to facilitate effective analysis of the large amount of biological data. However, with much of the biological knowledge represented in the literature in the form of natural text, analysis and interpretation of high-throughput data has not reached its potential effectiveness. In this paper, we describe our solution in employing text mining as a technique in finding scientific information for target and biomarker discovery from the biomedical literature. Our approach utilises natural language processing techniques to capture linguistic patterns for the extraction of biological knowledge from text. Additionally, we discuss how the extracted knowledge is used for the analysis of biological data such as next-generation sequencing and gene expression data.
MeSH term(s)	Computational Biology/methods ; Data Mining/methods ; Drug Design ; Drug Industry/trends ; Gene Expression Profiling ; Genome, Human ; Humans ; Inflammation/drug therapy ; Mutation ; Precision Medicine/methods ; Reproducibility of Results ; Software ; Tissue Distribution
Language	English
Publishing date	2015-05-06
Publishing country	Switzerland
Document type	Journal Article
ISSN	1748-5673
ISSN	1748-5673
DOI	10.1504/ijdmb.2014.064888
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Neurologie.

Perrenoud, Matthieu / Pantazou, Vasiliki / Michel, Patrik / Hirt, Lorenz / Ryvlin, Philippe / Theaudin, Marie / Rouaud, Olivier / Benninger, David / Novy, Jan / Rossetti, Andrea O / Kuntzer, Thierry / Diserens, Karin / Pasquier, Renaud Du

Revue medicale suisse

2020 Volume 16, Issue 676-7, Page(s) 68–71

Abstract: New studies confirm the possibility of late thrombolysis. Meta-analyses have confirmed that CGRP inhibitors are efficacious for migraines. Cladribine is a new oral treatment for relapsing-remitting multiple sclerosis. Limbic-predominant age-related TDP- ... ...

Title translation	Neurology 2019.
Abstract	New studies confirm the possibility of late thrombolysis. Meta-analyses have confirmed that CGRP inhibitors are efficacious for migraines. Cladribine is a new oral treatment for relapsing-remitting multiple sclerosis. Limbic-predominant age-related TDP-43 encephalopathy (LATE) is a new clinical entity accounting for cognitive decline in old patients. The timing of levodopa introduction has no effect on the long-term course of idiopathic Parkinson's disease. Hypophosphatemia helps distinguish between seizures and syncopes in the emergency department. A second course of intravenous immunoglobulins provides no benefit for severe Guillain Barre syndrome. Outdoor therapy improves clinical scales in patients with disorder of consciousness. Ultrasound guided lumbar puncture improves the yield of the procedure.
MeSH term(s)	Cladribine ; Guillain-Barre Syndrome ; Humans ; Immunoglobulins, Intravenous ; Multiple Sclerosis, Relapsing-Remitting ; Neurology/trends
Chemical Substances	Immunoglobulins, Intravenous ; Cladribine (47M74X9YT5)
Language	French
Publishing date	2020-01-21
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2177010-4
ISSN	1660-9379
ISSN	1660-9379
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Neurologie.

Anichini, Angelica / Salvioni Chiabotti, Paolo / Bally, Julien / Castro Jimenez, Mayte / Démonet, Jean-François / Di Virgilio, Gabriella / Hirt, Lorenz / Hottinger, Andreas / Kuntzer, Thierry / Michel, Patrik / Novy, Jan / Pot Kreis, Caroline / Rossetti, Andrea O / Rouaud, Olivier / Théaudin, Marie / Du Pasquier, Renaud

Revue medicale suisse

2021 Volume 17, Issue 723, Page(s) 196–200

Abstract: Significant developments were published in 2020 in the field of blood biomarkers in Alzheimer's disease. Several studies helped to define more accurately the management of status epilepticus and of epilepsy in women of childbearing age. The new Swiss ... ...

Title translation	Recent Advances in Neurology.
Abstract	Significant developments were published in 2020 in the field of blood biomarkers in Alzheimer's disease. Several studies helped to define more accurately the management of status epilepticus and of epilepsy in women of childbearing age. The new Swiss guidelines for the pre-hospital management of acute stroke were issued, as are new targets for stroke prevention. Numerous advances concerning the management of NMO-SD (NeuroMyelitis Optica Spectrum Disorder) were published. Different neurological presentations linked to the COVID-19 pandemic were described (central and peripheral). Several studies confirmed the effectiveness of new migraine treatments (including anti-CGRP). New pharmacological therapies are available for Parkinson's disease.
MeSH term(s)	COVID-19 ; Female ; Humans ; Neurology ; Neuromyelitis Optica/epidemiology ; Pandemics ; SARS-CoV-2
Language	French
Publishing date	2021-01-28
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2177010-4
ISSN	1660-9379
ISSN	1660-9379
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Prise en charge des polyradiculoneuropathies aiguës et chroniques.

Novy, Jan / Kuntzer, Thierry

Revue medicale suisse

2007 Volume 3, Issue 110, Page(s) 1166–1169

Abstract: Acute and chronic polyradiculoneuropathies are described in this review, both treatable uncommon forms of neuropathies. These diseases associate proximal and distal sensitivomotor involvement. Their onset can be acute or chronic. Both forms are dysimmune. ...

Title translation	Management of the acute and chronic polyradiculoneuropathies.
Abstract	Acute and chronic polyradiculoneuropathies are described in this review, both treatable uncommon forms of neuropathies. These diseases associate proximal and distal sensitivomotor involvement. Their onset can be acute or chronic. Both forms are dysimmune. Their treatment are based on immuno-modulation and immuno-suppression in chronic forms. Work-up sequence and therapeutical modes are discussed in the light of recently published data, with a special interest on pain management and early rehabilitation.
MeSH term(s)	Guillain-Barre Syndrome/diagnosis ; Guillain-Barre Syndrome/physiopathology ; Guillain-Barre Syndrome/therapy ; Humans ; Polyradiculoneuropathy, Chronic Inflammatory Demyelinating/diagnosis ; Polyradiculoneuropathy, Chronic Inflammatory Demyelinating/therapy ; Prognosis
Language	French
Publishing date	2007-05-09
Publishing country	Switzerland
Document type	English Abstract ; Journal Article ; Review
ZDB-ID	2177010-4
ISSN	1660-9379
ISSN	1660-9379
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: BiNA: a visual analytics tool for biological network data.

Gerasch, Andreas / Faber, Daniel / Küntzer, Jan / Niermann, Peter / Kohlbacher, Oliver / Lenhof, Hans-Peter / Kaufmann, Michael

PloS one

2014 Volume 9, Issue 2, Page(s) e87397

Abstract: Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and ... ...

Abstract	Interactive visual analysis of biological high-throughput data in the context of the underlying networks is an essential task in modern biomedicine with applications ranging from metabolic engineering to personalized medicine. The complexity and heterogeneity of data sets require flexible software architectures for data analysis. Concise and easily readable graphical representation of data and interactive navigation of large data sets are essential in this context. We present BiNA--the Biological Network Analyzer--a flexible open-source software for analyzing and visualizing biological networks. Highly configurable visualization styles for regulatory and metabolic network data offer sophisticated drawings and intuitive navigation and exploration techniques using hierarchical graph concepts. The generic projection and analysis framework provides powerful functionalities for visual analyses of high-throughput omics data in the context of networks, in particular for the differential analysis and the analysis of time series data. A direct interface to an underlying data warehouse provides fast access to a wide range of semantically integrated biological network databases. A plugin system allows simple customization and integration of new analysis algorithms or visual representations. BiNA is available under the 3-clause BSD license at http://bina.unipax.info/.
MeSH term(s)	Algorithms ; Computer Graphics ; Data Mining/methods ; Database Management Systems ; Databases, Factual ; Gene Regulatory Networks ; Humans ; Metabolic Networks and Pathways ; Protein Interaction Mapping
Language	English
Publishing date	2014-02-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0087397
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Roche Cancer Genome Database 2.0.

Küntzer, Jan / Maisel, Daniela / Lenhof, Hans-Peter / Klostermann, Stefan / Burtscher, Helmut

BMC medical genomics

2011 Volume 4, Page(s) 43

Abstract: Background: Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic DNA sequence mutations. Some of these mutations can be critical for the development of a tumor and can be useful to characterize tumor types or ... ...

Abstract	Background: Cancer is a disease of genome alterations that arise through the acquisition of multiple somatic DNA sequence mutations. Some of these mutations can be critical for the development of a tumor and can be useful to characterize tumor types or predict outcome. Description: We have constructed an integrated biological information system termed the Roche Cancer Genome Database (RCGDB) combining different human mutation databases already publicly available. This data is further extended by hand-curated information from publications.The current version of the RCGDB provides a user-friendly graphical interface that gives access to the data in different ways: (1) Single interactive search by genes, samples, cell lines, diseases, as well as pathways, (2) batch searches for genes and cell lines, (3) customized searches for regularly occurring requests, and (4) an advanced query interface enabling the user to query for samples and mutations by various filter criteria. Conclusion: The interfaces of the presented database enable the user to search and view mutations in an intuitive and straight-forward manner. The database is freely accessible at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/.
MeSH term(s)	Databases, Genetic ; ErbB Receptors/genetics ; Genome, Human/genetics ; Humans ; Mutation/genetics ; Neoplasms/genetics ; Receptor, ErbB-2/genetics ; Search Engine
Chemical Substances	ERBB2 protein, human (EC 2.7.10.1) ; ErbB Receptors (EC 2.7.10.1) ; Receptor, ErbB-2 (EC 2.7.10.1)
Language	English
Publishing date	2011-05-17
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2411865-5
ISSN	1755-8794 ; 1755-8794
ISSN (online)	1755-8794
ISSN	1755-8794
DOI	10.1186/1755-8794-4-43
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Roche Cancer Genome Database (RCGDB)

Küntzer, Jan / Eggle, Daniela / Lenhof, Hans-Peter / Burtscher, Helmut / Klostermann, Stefan

Human mutation. 2010 Apr., v. 31, no. 4

2010

Abstract: Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with ... ...

Abstract	Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with efficient data acquisition methods have resulted in an explosion of available cancer genome-related data. Despite the technological progress and increase of data, improvements in the application area, for example, drug target discovery, have failed to keep pace with increased research and development spending. One reason for this discrepancy is the ever increasing number of databases and the absence of a unified access to the mutation data. Currently, researchers typically have to browse several, often highly specialized databases to obtain the required information. A more complete understanding of relations and dependencies between mutations and cancer, however, requires the availability of an efficient integrative cancer genome information system. To facilitate this, we developed the Roche Cancer Genome Database (RCGDB), a freely available biological information system integrating different kinds of mutation data. The database is the first comprehensive integration of disparate cancer genome data like single nucleotide variants, single nucleotide polymorphisms, and chromosomal aberrations (CGH and FISH). RCGDB is freely accessible via a Google-like Web interface at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/. Hum Mutat 31:1-7, 2010.
Language	English
Dates of publication	2010-04
Size	p. 407-413.
Publishing place	Wiley Subscription Services, Inc., A Wiley Company
Document type	Article
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.21207
Database	NAL-Catalogue (AGRICOLA)

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Article: Neurologie.

Eskioglou, Elissavet / Benninger, David / Di Virgilio, Gabriella / Hirt, Lorenz / Kuntzer, Thierry / Michel, Patrik / Novy, Jan / Rossetti, Andrea O / Rouaud, Olivier / Ryvlin, Philippe / Theaudin, Marie / Du Pasquier, Renaud

Revue medicale suisse

2019 Volume 15, Issue N° 632-633, Page(s) 74–77

Abstract: Thrombolysis and late thrombectomy can be performed in case of compatible radiological imaging. Anti-CGRP monoclonal antibodies seem more effective for the treatment of migraine. Siponimod can reduce significantly disability progression in secondarily ... ...

Title translation	Neurology.
Abstract	Thrombolysis and late thrombectomy can be performed in case of compatible radiological imaging. Anti-CGRP monoclonal antibodies seem more effective for the treatment of migraine. Siponimod can reduce significantly disability progression in secondarily progressive MS. Brand-to-generic levetiracetam switching does not cause recrudescence of epileptic seizures. A new definition of Alzheimer's disease using biomarkers of cerebrospinal fluid (CSF) and imaging provides a better understanding of the underlying mechanisms. The use of levodopa-carbidopa intestinal gel and a subcutaneous apomorphine infusion allow a reduction of motor fluctuations in Parkinson's disease. Eculizumab appears as an alternative treatment in severe forms of myasthenia gravis.
MeSH term(s)	Antiparkinson Agents/therapeutic use ; Disease Progression ; Drug Combinations ; Humans ; Levodopa/therapeutic use ; Neurology/trends ; Parkinson Disease/drug therapy
Chemical Substances	Antiparkinson Agents ; Drug Combinations ; Levodopa (46627O600J)
Language	French
Publishing date	2019-02-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2177010-4
ISSN	1660-9379
ISSN	1660-9379
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: The Roche Cancer Genome Database (RCGDB).

Küntzer, Jan / Eggle, Daniela / Lenhof, Hans-Peter / Burtscher, Helmut / Klostermann, Stefan

Human mutation

2010 Volume 31, Issue 4, Page(s) 407–413

Abstract	Sequence variations are being studied for a better understanding of the mechanism and development of cancer as a mutation-driven disease. The systematic sequencing of genes in tumors and technological advances in high-throughput techniques combined with efficient data acquisition methods have resulted in an explosion of available cancer genome-related data. Despite the technological progress and increase of data, improvements in the application area, for example, drug target discovery, have failed to keep pace with increased research and development spending. One reason for this discrepancy is the ever increasing number of databases and the absence of a unified access to the mutation data. Currently, researchers typically have to browse several, often highly specialized databases to obtain the required information. A more complete understanding of relations and dependencies between mutations and cancer, however, requires the availability of an efficient integrative cancer genome information system. To facilitate this, we developed the Roche Cancer Genome Database (RCGDB), a freely available biological information system integrating different kinds of mutation data. The database is the first comprehensive integration of disparate cancer genome data like single nucleotide variants, single nucleotide polymorphisms, and chromosomal aberrations (CGH and FISH). RCGDB is freely accessible via a Google-like Web interface at http://rcgdb.bioinf.uni-sb.de/MutomeWeb/.
MeSH term(s)	Cell Line, Tumor ; Databases, Genetic ; Genes, Neoplasm/genetics ; Genome, Human/genetics ; Humans ; Internet ; Mutation/genetics ; Neoplasms/genetics ; Polymorphism, Single Nucleotide/genetics ; Receptor, Epidermal Growth Factor/genetics
Chemical Substances	Receptor, Epidermal Growth Factor (EC 2.7.10.1)
Language	English
Publishing date	2010-04
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.21207
Database	MEDical Literature Analysis and Retrieval System OnLINE

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