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Article ; Online: Noncoding RNAs as effective markers in cancer-care management.

Raimondi, Ivan / Huarte, Maite

2017 Volume 23, Issue 10, Page(s) 1122–1123

MeSH term(s)	Carcinoma, Basal Cell ; Humans ; Microfilament Proteins ; Mutation ; RNA ; RNA, Untranslated
Chemical Substances	ACTRT1 protein, human ; Microfilament Proteins ; RNA, Untranslated ; RNA (63231-63-0)
Language	English
Publishing date	2017-09-29
Publishing country	United States
Document type	Journal Article ; Comment
ZDB-ID	1220066-9
ISSN	1546-170X ; 1078-8956
ISSN (online)	1546-170X
ISSN	1078-8956
DOI	10.1038/nm.4423
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Zs.A 4212: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.

Stuart, Tim / Hao, Stephanie / Zhang, Bingjie / Mekerishvili, Levan / Landau, Dan A / Maniatis, Silas / Satija, Rahul / Raimondi, Ivan

Nature biotechnology

2022 Volume 41, Issue 6, Page(s) 806–812

Abstract: Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single ... ...

Abstract	Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single experiment at single-cell resolution. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), an assay capable of measuring the genome-wide presence of up to three histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq uses recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk-cell and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in human immune cells. We also extend NTT-seq to enable simultaneous profiling of cell surface protein expression and multimodal chromatin states to study cells of the immune system.
MeSH term(s)	Humans ; Chromatin/genetics ; DNA/metabolism ; Sequence Analysis, DNA/methods ; Genome ; Protein Binding ; High-Throughput Nucleotide Sequencing ; Single-Cell Analysis
Chemical Substances	Chromatin ; DNA (9007-49-2)
Language	English
Publishing date	2022-12-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01588-5
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro.

Zhang, Bingjie / Srivastava, Avi / Mimitou, Eleni / Stuart, Tim / Raimondi, Ivan / Hao, Yuhan / Smibert, Peter / Satija, Rahul

Nature biotechnology

2022 Volume 40, Issue 8, Page(s) 1220–1230

Abstract: Technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization, but the sparsity of the measurements and integrating multiple binding maps represent substantial challenges. Here ... ...

Abstract	Technologies that profile chromatin modifications at single-cell resolution offer enormous promise for functional genomic characterization, but the sparsity of the measurements and integrating multiple binding maps represent substantial challenges. Here we introduce single-cell (sc)CUT&Tag-pro, a multimodal assay for profiling protein-DNA interactions coupled with the abundance of surface proteins in single cells. In addition, we introduce single-cell ChromHMM, which integrates data from multiple experiments to infer and annotate chromatin states based on combinatorial histone modification patterns. We apply these tools to perform an integrated analysis across nine different molecular modalities in circulating human immune cells. We demonstrate how these two approaches can characterize dynamic changes in the function of individual genomic elements across both discrete cell states and continuous developmental trajectories, nominate associated motifs and regulators that establish chromatin states and identify extensive and cell-type-specific regulatory priming. Finally, we demonstrate how our integrated reference can serve as a scaffold to map and improve the interpretation of additional scCUT&Tag datasets.
MeSH term(s)	Chromatin/genetics ; Chromatin Immunoprecipitation ; DNA ; Genomics ; Histones/genetics ; Histones/metabolism ; Humans
Chemical Substances	Chromatin ; Histones ; DNA (9007-49-2)
Language	English
Publishing date	2022-03-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1311932-1
ISSN	1546-1696 ; 1087-0156
ISSN (online)	1546-1696
ISSN	1087-0156
DOI	10.1038/s41587-022-01250-0
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Zs.A 2167: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
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Article: The multidimensional mechanisms of long noncoding RNA function

Marchese, Francesco P / Huarte, Maite / Raimondi, Ivan

Genome biology. 2017 Dec., v. 18, no. 1

2017

Abstract: A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that ... ...

Abstract	A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.
Keywords	cell nucleus ; gene expression ; genes ; non-coding RNA ; proteins ; transcription (genetics)
Language	English
Dates of publication	2017-12
Size	p. 206.
Publishing place	BioMed Central
Document type	Article
Note	Review
ZDB-ID	2040529-7
ISSN	1474-760X ; 1465-6914 ; 1465-6906
ISSN (online)	1474-760X ; 1465-6914
ISSN	1465-6906
DOI	10.1186/s13059-017-1348-2
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: The multidimensional mechanisms of long noncoding RNA function.

Marchese, Francesco P / Raimondi, Ivan / Huarte, Maite

Genome biology

2017 Volume 18, Issue 1, Page(s) 206

Abstract	A major shift in our understanding of genome regulation has emerged recently. It is now apparent that the majority of cellular transcripts do not code for proteins, and many of them are long noncoding RNAs (lncRNAs). Increasingly, studies suggest that lncRNAs regulate gene expression through diverse mechanisms. We review emerging mechanistic views of lncRNAs in gene regulation in the cell nucleus. We discuss the functional interactions that lncRNAs establish with other molecules as well as the relationship between lncRNA transcription and function. While some of these mechanisms are specific to lncRNAs, others might be shared with other types of genes.
MeSH term(s)	Animals ; Chromatin/metabolism ; DNA/chemistry ; DNA/metabolism ; DNA-Binding Proteins/metabolism ; Enhancer Elements, Genetic ; Gene Expression Regulation ; RNA, Long Noncoding/metabolism ; RNA-Binding Proteins/metabolism ; Transcription, Genetic
Chemical Substances	Chromatin ; DNA-Binding Proteins ; RNA, Long Noncoding ; RNA-Binding Proteins ; DNA (9007-49-2)
Language	English
Publishing date	2017-10-31
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2040529-7
ISSN	1474-760X ; 1474-760X
ISSN (online)	1474-760X
ISSN	1474-760X
DOI	10.1186/s13059-017-1348-2
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Article ; Online: Efficient and safe therapeutic use of paired Cas9-nickases for primary hyperoxaluria type 1.

Torella, Laura / Klermund, Julia / Bilbao-Arribas, Martin / Tamayo, Ibon / Andrieux, Geoffroy / Chmielewski, Kay O / Vales, Africa / Olagüe, Cristina / Moreno-Luqui, Daniel / Raimondi, Ivan / Abad, Amaya / Torrens-Baile, Julen / Salido, Eduardo / Huarte, Maite / Hernaez, Mikel / Boerries, Melanie / Cathomen, Toni / Zabaleta, Nerea / Gonzalez-Aseguinolaza, Gloria

EMBO molecular medicine

2024 Volume 16, Issue 1, Page(s) 112–131

Abstract: The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. ... ...

Abstract	The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored the use of AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target the Hao1 gene for the treatment of primary hyperoxaluria type 1 (PH1). Our study demonstrated effective Hao1 gene disruption, a significant decrease in glycolate oxidase expression, and a therapeutic effect in PH1 mice. The assessment of undesired genetic modifications through CIRCLE-seq and CAST-Seq analyses revealed neither off-target activity nor chromosomal translocations. Importantly, the use of paired-D10ASaCas9 resulted in a significant reduction in AAV integration at the target site compared to SaCas9 nuclease. In addition, our study highlights the limitations of current analytical tools in characterizing modifications introduced by paired D10ASaCas9, necessitating the development of a custom pipeline for more accurate characterization. These results describe a positive advance towards a safe and effective potential long-term treatment for PH1 patients.
MeSH term(s)	Humans ; Animals ; Mice ; CRISPR-Cas Systems ; Deoxyribonuclease I/genetics ; Deoxyribonuclease I/metabolism ; Gene Editing ; Hyperoxaluria, Primary/genetics ; Hyperoxaluria, Primary/therapy
Chemical Substances	Deoxyribonuclease I (EC 3.1.21.1)
Language	English
Publishing date	2024-01-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2467145-9
ISSN	1757-4684 ; 1757-4676
ISSN (online)	1757-4684
ISSN	1757-4676
DOI	10.1038/s44321-023-00008-8
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Article ; Online: A lncRNA-SWI/SNF complex crosstalk controls transcriptional activation at specific promoter regions.

Grossi, Elena / Raimondi, Ivan / Goñi, Enrique / González, Jovanna / Marchese, Francesco P / Chapaprieta, Vicente / Martín-Subero, José I / Guo, Shuling / Huarte, Maite

Nature communications

2020 Volume 11, Issue 1, Page(s) 936

Abstract: LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the role of lncRNAs in gene activation by profiling the RNA interactome of SMARCB1-containing SWI/SNF ... ...

Abstract	LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the role of lncRNAs in gene activation by profiling the RNA interactome of SMARCB1-containing SWI/SNF complexes in proliferating and senescent conditions. The isolation of SMARCB1-associated transcripts, together with chromatin profiling, shows prevalent association to active regions where SMARCB1 differentially binds locally transcribed RNAs. We identify SWINGN, a lncRNA interacting with SMARCB1 exclusively in proliferating conditions, exerting a pro-oncogenic role in some tumor types. SWINGN is transcribed from an enhancer and modulates the activation of GAS6 oncogene as part of a topologically organized region, as well as a larger network of pro-oncogenic genes by favoring SMARCB1 binding. Our results indicate that SWINGN influences the ability of the SWI/SNF complexes to drive epigenetic activation of specific promoters, suggesting a SWI/SNF-RNA cooperation to achieve optimal transcriptional activation.
MeSH term(s)	Animals ; Apoptosis/genetics ; Carcinogenesis ; Cell Proliferation/genetics ; Datasets as Topic ; Female ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; HCT116 Cells ; HEK293 Cells ; Humans ; Intercellular Signaling Peptides and Proteins/genetics ; Mice ; Neoplasms/genetics ; Neoplasms/pathology ; Promoter Regions, Genetic/genetics ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA, Small Interfering/metabolism ; RNA-Seq ; SMARCB1 Protein/metabolism ; Transcriptional Activation ; Xenograft Model Antitumor Assays
Chemical Substances	Intercellular Signaling Peptides and Proteins ; RNA, Long Noncoding ; RNA, Small Interfering ; SMARCB1 Protein ; SMARCB1 protein, human ; growth arrest-specific protein 6
Language	English
Publishing date	2020-02-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-020-14623-3
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Article ; Online: Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay.

Lion, Mattia / Raimondi, Ivan / Donati, Stefano / Jousson, Olivier / Ciribilli, Yari / Inga, Alberto

PloS one

2015 Volume 10, Issue 2, Page(s) e0116177

Abstract: Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary ... ...

Abstract	Co-evolution of transcription factors (TFs) with their respective cis-regulatory network enhances functional diversity in the course of evolution. We present a new approach to investigate transactivation capacity of sequence-specific TFs in evolutionary studies. Saccharomyces cerevisiae was used as an in vivo test tube and p53 proteins derived from human and five commonly used animal models were chosen as proof of concept. p53 is a highly conserved master regulator of environmental stress responses. Previous reports indicated conserved p53 DNA binding specificity in vitro, even for evolutionary distant species. We used isogenic yeast strains where p53-dependent transactivation was measured towards chromosomally integrated p53 response elements (REs). Ten REs were chosen to sample a wide range of DNA binding affinity and transactivation capacity for human p53 and proteins were expressed at two levels using an inducible expression system. We showed that the assay is amenable to study thermo-sensitivity of frog p53, and that chimeric constructs containing an ectopic transactivation domain could be rapidly developed to enhance the activity of proteins, such as fruit fly p53, that are poorly effective in engaging the yeast transcriptional machinery. Changes in the profile of relative transactivation towards the ten REs were measured for each p53 protein and compared to the profile obtained with human p53. These results, which are largely independent from relative p53 protein levels, revealed widespread evolutionary divergence of p53 transactivation specificity, even between human and mouse p53. Fruit fly and human p53 exhibited the largest discrimination among REs while zebrafish p53 was the least selective.
MeSH term(s)	Amino Acid Sequence ; Animals ; Base Sequence ; Cluster Analysis ; Drosophila ; Evolution, Molecular ; Humans ; Isoquinolines ; Mice ; Molecular Sequence Data ; Phylogeny ; Plasmids/genetics ; Response Elements/genetics ; Saccharomyces cerevisiae ; Sequence Alignment ; Sequence Analysis, DNA ; Species Specificity ; Transcriptional Activation/genetics ; Tumor Suppressor Protein p53/genetics ; Xenopus laevis ; Zebrafish
Chemical Substances	Isoquinolines ; Tumor Suppressor Protein p53 ; lucifer yellow (9654F8OVKE)
Language	English
Publishing date	2015
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0116177
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Article ; Online: The structure formed by inverted repeats in p53 response elements determines the transactivation activity of p53 protein.

Brázda, Václav / Čechová, Jana / Battistin, Michele / Coufal, Jan / Jagelská, Eva B / Raimondi, Ivan / Inga, Alberto

Biochemical and biophysical research communications

2017 Volume 483, Issue 1, Page(s) 516–521

Abstract: The TP53 gene is the most frequently mutated gene in human cancer and p53 protein plays a crucial role in gene expression and cancer protection. Its role is manifested by interactions with other proteins and DNA. p53 is a transcription factor that binds ... ...

Abstract	The TP53 gene is the most frequently mutated gene in human cancer and p53 protein plays a crucial role in gene expression and cancer protection. Its role is manifested by interactions with other proteins and DNA. p53 is a transcription factor that binds to DNA response elements (REs). Due to the palindromic nature of the consensus binding site, several p53-REs have the potential to form cruciform structures. However, the influence of cruciform formation on the activity of p53-REs has not been evaluated. Therefore, we prepared sets of p53-REs with identical theoretical binding affinity in their linear state, but different probabilities to form extra helical structures, for in vitro and in vivo analyses. Then we evaluated the presence of cruciform structures when inserted into plasmid DNA and employed a yeast-based assay to measure transactivation potential of these p53-REs cloned at a chromosomal locus in isogenic strains. We show that transactivation in vivo correlated more with relative propensity of an RE to form cruciforms than to its predicted in vitro DNA binding affinity for wild type p53. Structural features of p53-REs could therefore be an important determinant of p53 transactivation function.
MeSH term(s)	Chromatin/genetics ; Computer Simulation ; Inverted Repeat Sequences ; Mutation ; Response Elements ; Transcriptional Activation ; Tumor Suppressor Protein p53/chemistry ; Tumor Suppressor Protein p53/genetics ; Tumor Suppressor Protein p53/metabolism ; Yeasts/genetics
Chemical Substances	Chromatin ; Tumor Suppressor Protein p53
Language	English
Publishing date	2017-01-29
Publishing country	United States
Document type	Journal Article
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2016.12.113
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Article ; Online: Analysis of copy number alterations reveals the lncRNA ALAL-1 as a regulator of lung cancer immune evasion.

Athie, Alejandro / Marchese, Francesco P / González, Jovanna / Lozano, Teresa / Raimondi, Ivan / Juvvuna, Prasanna Kumar / Abad, Amaya / Marin-Bejar, Oskar / Serizay, Jacques / Martínez, Dannys / Ajona, Daniel / Pajares, Maria Jose / Sandoval, Juan / Montuenga, Luis M / Kanduri, Chandrasekhar / Lasarte, Juan J / Huarte, Maite

The Journal of cell biology

2020 Volume 219, Issue 9

Abstract: Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified in ... ...

Abstract	Cancer is characterized by genomic instability leading to deletion or amplification of oncogenes or tumor suppressors. However, most of the altered regions are devoid of known cancer drivers. Here, we identify lncRNAs frequently lost or amplified in cancer. Among them, we found amplified lncRNA associated with lung cancer-1 (ALAL-1) as frequently amplified in lung adenocarcinomas. ALAL-1 is also overexpressed in additional tumor types, such as lung squamous carcinoma. The RNA product of ALAL-1 is able to promote the proliferation and tumorigenicity of lung cancer cells. ALAL-1 is a TNFα- and NF-κB-induced cytoplasmic lncRNA that specifically interacts with SART3, regulating the subcellular localization of the protein deubiquitinase USP4 and, in turn, its function in the cell. Interestingly, ALAL-1 expression inversely correlates with the immune infiltration of lung squamous tumors, while tumors with ALAL-1 amplification show lower infiltration of several types of immune cells. We have thus unveiled a pro-oncogenic lncRNA that mediates cancer immune evasion, pointing to a new target for immune potentiation.
MeSH term(s)	A549 Cells ; Adenocarcinoma of Lung/genetics ; Antigens, Neoplasm/genetics ; Carcinoma, Squamous Cell/genetics ; Cell Line, Tumor ; Cell Proliferation/genetics ; DNA Copy Number Variations/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Humans ; Immune Evasion/genetics ; Lung Neoplasms/genetics ; NF-kappa B/genetics ; Oncogenes/genetics ; RNA, Long Noncoding/genetics ; Ubiquitin-Specific Proteases/genetics
Chemical Substances	Antigens, Neoplasm ; NF-kappa B ; RNA, Long Noncoding ; Ubiquitin-Specific Proteases (EC 3.4.19.12)
Language	English
Publishing date	2020-08-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201908078
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