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Article ; Online: Advancements in bioinformatics and computational biology: 15th annual Polish Bioinformatic Society Symposium.

Zyla, Joanna / Tobiasz, Joanna / Mika, Justyna / Łabaj, Paweł P / Gruca, Aleksandra

Bioinformatics advances

2024 Volume 4, Issue 1, Page(s) vbad187

Abstract: The Polish Bioinformatic Society (PTBI) Symposium convenes annually at leading Polish Universities, and in 2023, the Silesian University of Technology hosted participants from all over the world. The 15th PTBI Symposium, spanning a 3-day duration and ... ...

Abstract	The Polish Bioinformatic Society (PTBI) Symposium convenes annually at leading Polish Universities, and in 2023, the Silesian University of Technology hosted participants from all over the world. The 15th PTBI Symposium, spanning a 3-day duration and divided into four scientific sessions, gathered around 100 participants and centered on research related to machine learning in biomedicine, RNA structure algorithms, next-generation sequencing methods, and microbiome analysis but was not limited to only those topics. The meeting also recognized outstanding research conducted by young scientists by awarding the best poster and best talk. Finally, the awards for the best PhD, MSc, and BSc thesis in bioinformatics defended in Poland were given. This report summarizes the key highlights and outcomes of the meeting.
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbad187
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Article ; Online: Sex- and age-specific aspects of human peripheral T-cell dynamics.

Mika, Justyna / Yoshida, Kengo / Kusunoki, Yoichiro / Candéias, Serge M / Polanska, Joanna

Frontiers in immunology

2023 Volume 14, Page(s) 1224304

Abstract: Background: The diversity of the antigenic T cell receptor (TCR) repertoire clonally expressed on T lymphocytes is a key element of the adaptive immune system protective functions. A decline in diversity in the older adults is associated with health ... ...

Abstract	Background: The diversity of the antigenic T cell receptor (TCR) repertoire clonally expressed on T lymphocytes is a key element of the adaptive immune system protective functions. A decline in diversity in the older adults is associated with health deterioration. This diversity is generated by the rearrangement of TRB genes coding for TCR chains during lymphocyte differentiation in the thymus, but is essentially maintained by peripheral T lymphocytes proliferation for most of life. Deep sequencing of rearranged TRB genes from blood cells allows the monitoring of peripheral T cell repertoire dynamics. We analysed two aspects of rearranged TRB diversity, related to T lymphocyte proliferation and to the distribution of the T cell clone size, in a collection of repertoires obtained from 1 to 74 years-old donors. Results: Our results show that peripheral T lymphocytes expansion differs according to the recombination status of their TRB loci. Their proliferation rate changes with age, with different patterns in men and women. T cell clone size becomes more heterogeneous with time, and, in adults, is always more even in women. Importantly, a longitudinal analysis of TRB repertoires obtained at ten years intervals from individual men and women confirms the findings of this cross-sectional study. Conclusions: Peripheral T lymphocyte proliferation partially depends on their thymic developmental history. The rate of proliferation of T cells differing in their TRB rearrangement status is different in men and women before the age of 18 years old, but similar thereafter.
MeSH term(s)	Male ; Humans ; Female ; Aged ; Adolescent ; Infant ; Child, Preschool ; Child ; Young Adult ; Adult ; Middle Aged ; T-Lymphocytes ; Cross-Sectional Studies ; Thymus Gland ; Receptors, Antigen, T-Cell/genetics ; Age Factors
Chemical Substances	Receptors, Antigen, T-Cell
Language	English
Publishing date	2023-10-13
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1224304
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Article: The mutation profile of differentiated thyroid cancer coexisting with undifferentiated anaplastic cancer resembles that of anaplastic thyroid cancer but not that of archetypal differentiated thyroid cancer

Mika, Justyna / Łabaj, Wojciech / Chekan, Mykola / Abramowicz, Agata / Pietrowska, Monika / Polański, Andrzej / Widłak, Piotr

Journal of applied genetics. 2021 Feb., v. 62, no. 1

2021

Abstract: Differentiated thyroid cancer (DTC) has one of the lowest cancer mutational burdens, while anaplastic thyroid cancer (ATC) has a much higher mutation frequency. A fraction of ATC has an associated differentiated component, which suggests the coevolution ... ...

Abstract	Differentiated thyroid cancer (DTC) has one of the lowest cancer mutational burdens, while anaplastic thyroid cancer (ATC) has a much higher mutation frequency. A fraction of ATC has an associated differentiated component, which suggests the coevolution of both cancers. Here, we aimed to compare mutation frequency in coexisting ATC and DTC diagnosed concurrently in the same thyroid gland (3 cases) as well as in archetypal DTC and ATC alone (5 cases each). Single-nucleotide variations (SNV) and copy number variations (CNV) were analyzed in each case based on the next-generation sequencing data. We found a similar extent of mutational events, both SNV and CNV, in undifferentiated and differentiated components of thyroid cancers coexisting in one patient. The magnitude of these mutations was comparable to the level of mutations observed in ATC alone; yet, it was much higher than in archetypal DTC. This suggested that, despite histopathological features of differentiated tumors, molecular characteristics of such cancers coexisting with ATC and archetypal DTC could be significantly different. Pairwise comparison of mutational profiles of coexisting cancers enabled assumption on the possible evolution of both components, which appeared distinct in 3 analyzed cases. This included independent development of ATC and DTC diagnosed concurrently in two lobes of the same thyroid, as well as the development of anaplastic and differentiated cancer from the common ancestor that putatively gained a key driver mutation (BRAFⱽ⁶⁰⁰ᴱ or KRASQ⁶¹ᴿ), which was followed either by early or late molecular separation of both cancers.
Keywords	ancestry ; coevolution ; histopathology ; mutation ; mutation rate ; patients ; thyroid gland ; thyroid neoplasms
Language	English
Dates of publication	2021-02
Size	p. 115-120.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-020-00594-0
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Article ; Online: The mutation profile of differentiated thyroid cancer coexisting with undifferentiated anaplastic cancer resembles that of anaplastic thyroid cancer but not that of archetypal differentiated thyroid cancer.

Mika, Justyna / Łabaj, Wojciech / Chekan, Mykola / Abramowicz, Agata / Pietrowska, Monika / Polański, Andrzej / Widłak, Piotr

Journal of applied genetics

2020 Volume 62, Issue 1, Page(s) 115–120

Abstract	Differentiated thyroid cancer (DTC) has one of the lowest cancer mutational burdens, while anaplastic thyroid cancer (ATC) has a much higher mutation frequency. A fraction of ATC has an associated differentiated component, which suggests the coevolution of both cancers. Here, we aimed to compare mutation frequency in coexisting ATC and DTC diagnosed concurrently in the same thyroid gland (3 cases) as well as in archetypal DTC and ATC alone (5 cases each). Single-nucleotide variations (SNV) and copy number variations (CNV) were analyzed in each case based on the next-generation sequencing data. We found a similar extent of mutational events, both SNV and CNV, in undifferentiated and differentiated components of thyroid cancers coexisting in one patient. The magnitude of these mutations was comparable to the level of mutations observed in ATC alone; yet, it was much higher than in archetypal DTC. This suggested that, despite histopathological features of differentiated tumors, molecular characteristics of such cancers coexisting with ATC and archetypal DTC could be significantly different. Pairwise comparison of mutational profiles of coexisting cancers enabled assumption on the possible evolution of both components, which appeared distinct in 3 analyzed cases. This included independent development of ATC and DTC diagnosed concurrently in two lobes of the same thyroid, as well as the development of anaplastic and differentiated cancer from the common ancestor that putatively gained a key driver mutation (BRAF
MeSH term(s)	Adult ; Aged ; DNA Copy Number Variations ; Female ; Humans ; Male ; Middle Aged ; Mutation ; Thyroid Carcinoma, Anaplastic/genetics ; Thyroid Neoplasms/genetics
Language	English
Publishing date	2020-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	1235302-4
ISSN	2190-3883 ; 1234-1983
ISSN (online)	2190-3883
ISSN	1234-1983
DOI	10.1007/s13353-020-00594-0
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Article ; Online: Germline DNA Retention in Murine and Human Rearranged T Cell Receptor Gene Coding Joints: Alternative Recombination Signal Sequences and V(D)J Recombinase Errors.

Mika, Justyna / Kabacik, Sylwia / Badie, Christophe / Polanska, Joanna / Candéias, Serge M

Frontiers in immunology

2019 Volume 10, Page(s) 2637

Abstract: The genes coding for the antigenic T cell receptor (TR) subunits are assembled in thymocytes from discrete V, D, and J genes by a site-specific recombination process. A tight control of this activity is required to prevent potentially detrimental ... ...

Abstract	The genes coding for the antigenic T cell receptor (TR) subunits are assembled in thymocytes from discrete V, D, and J genes by a site-specific recombination process. A tight control of this activity is required to prevent potentially detrimental recombination events. V, D, and J genes are flanked by semi-conserved nucleotide motives called recombination signal sequences (RSSs). V(D)J recombination is initiated by the precise introduction of a DNA double-strand break exactly at the border of the genes and their RSSs by the RAG recombinase. RSSs are therefore physically separated from the coding region of the genes before assembly of a rearranged TR gene. During a high throughput profiling of TRB genes in mice, we identified rearranged TRB genes in which part or all of a flanking RSS was retained in V-D or D-J coding joints. In some instances, this retention of germline DNA resulted from the use of an upstream alternative RSS. However, we also identified TRB sequences where retention of germline DNA occurred in the absence of alternative RSS, suggesting that RAG activity was mis-targeted during recombination. Similar events were also identified in human rearranged TRB and TRG genes. The use of alternative RSSs during V(D)J recombination illustrates the complexity of RAG-RSSs interactions during V(D)J recombination. While the frequency of errors resulting from mis-targeted RAG activity is very low, we believe that these RAG errors may be at the origin of oncogenic translocations and are a threat for genetic stability in developing lymphocytes.
MeSH term(s)	Animals ; DNA ; Genes, T-Cell Receptor ; Humans ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Inbred CBA ; V(D)J Recombination ; VDJ Recombinases
Chemical Substances	DNA (9007-49-2) ; VDJ Recombinases (EC 2.7.7.-)
Language	English
Publishing date	2019-11-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2019.02637
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Article: Proteomic profile of melanoma cell-derived small extracellular vesicles in patients' plasma: a potential correlate of melanoma progression.

Pietrowska, Monika / Zebrowska, Aneta / Gawin, Marta / Marczak, Lukasz / Sharma, Priyanka / Mondal, Sujan / Mika, Justyna / Polańska, Joanna / Ferrone, Soldano / Kirkwood, John M / Widlak, Piotr / Whiteside, Theresa L

Journal of extracellular vesicles

2021 Volume 10, Issue 4, Page(s) e12063

Abstract: Molecular profiling of small extracellular vesicles (sEV) isolated from plasma of cancer patients emerges as promising strategy for biomarkers discovery. We investigated the proteomic profiles of sEV immunoselected using anti-CSPG4 antibodies from 15 ... ...

Abstract	Molecular profiling of small extracellular vesicles (sEV) isolated from plasma of cancer patients emerges as promising strategy for biomarkers discovery. We investigated the proteomic profiles of sEV immunoselected using anti-CSPG4 antibodies from 15 melanoma patients' plasma. The proteomes of sEV separated into melanoma cell-derived (MTEX) and non-malignant cell-derived (NMTEX) were compared using high-resolution mass spectrometry. Paired analysis identified the MTEX-associated profile of 16 proteins that discriminated MTEX from NMETEX. We also identified the MTEX profile that discriminated between seven patients with no evidence of melanoma (NED) after therapy and eight with progressive disease (PD). Among 75 MTEX proteins overexpressed in PD patients, PDCD6IP (ALIX) had the highest discriminating value, while CNTN1 (contactin-1) was upregulated only in MTEX of NED patients. This is the first report documenting that proteomes of tumour-derived sEV in patients' plasma discriminate cancer from non-cancer and identify proteins with potential to serve as prognostic biomarkers in melanoma.
MeSH term(s)	Adult ; Aged ; Biomarkers, Tumor/blood ; Chondroitin Sulfate Proteoglycans/immunology ; Chondroitin Sulfate Proteoglycans/metabolism ; Contactin 1/metabolism ; Disease Progression ; Exosomes/chemistry ; Exosomes/metabolism ; Extracellular Vesicles/chemistry ; Extracellular Vesicles/metabolism ; Female ; Humans ; Male ; Mass Spectrometry ; Melanoma/chemistry ; Melanoma/metabolism ; Membrane Proteins/immunology ; Membrane Proteins/metabolism ; Middle Aged ; Plasma/chemistry ; Plasma/metabolism ; Proteins/metabolism ; Proteome/metabolism
Chemical Substances	Biomarkers, Tumor ; CNTN1 protein, human ; CSPG4 protein, human ; Chondroitin Sulfate Proteoglycans ; Contactin 1 ; Membrane Proteins ; Proteins ; Proteome
Language	English
Publishing date	2021-02-11
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2683797-3
ISSN	2001-3078
ISSN	2001-3078
DOI	10.1002/jev2.12063
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Article ; Online: MicroRNA Profile of Exosomes and Parental Cells is Differently Affected by Ionizing Radiation.

Abramowicz, Agata / Łabaj, Wojciech / Mika, Justyna / Szołtysek, Katarzyna / Ślęzak-Prochazka, Izabella / Mielańczyk, Łukasz / Story, Michael D / Pietrowska, Monika / Polański, Andrzej / Widłak, Piotr

Radiation research

2020 Volume 194, Issue 2, Page(s) 133–142

Abstract: Exosomes are key mediators of cell-to-cell communication involved in different aspects of the response to ionizing radiation. The functional role of exosomes depends on their molecular cargo, including protein and miRNA content. In this work, we compared ...

Abstract	Exosomes are key mediators of cell-to-cell communication involved in different aspects of the response to ionizing radiation. The functional role of exosomes depends on their molecular cargo, including protein and miRNA content. In this work, we compared the miRNA profile of cells exposed to a high-dose of radiation and the exosomes released by those cells. FaDu cells (derived from human head and neck cancer) were exposed to 2 and 8 Gy doses, exosomes were purified from culture media at 36 h postirradiation using a combination of differential centrifugation, ultrafiltration and precipitation, then microRNA was analyzed using the RNA-seq approach. There were 439 miRNA species quantified, and significant differences in their relative abundance were observed between the cells and exosomes; several low-abundance miRNAs were over-represented while high-abundance miRNA were under-represented in exosomes. There were a few miRNA species markedly affected in irradiated cells and in exosomes released by these cells. However, markedly different radiation-induced effects were observed in both miRNA sets, which could be exemplified by miR-3168 significantly downregulated in cells and upregulated in exosomes. On the other hand, both 2 and 8 Gy radiation doses induced similar effects. Radiation-affected miRNA species present in exosomes are linked to genes involved in the DNA damage and cytokine-mediated response, which may suggest their hypothetical role in the exosome-mediated radiation-induced bystander effect reported elsewhere.
MeSH term(s)	Cell Communication/radiation effects ; Cell Line ; Computational Biology ; Exosomes/metabolism ; Exosomes/radiation effects ; Humans ; MicroRNAs/genetics
Chemical Substances	MicroRNAs
Language	English
Publishing date	2020-05-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80322-4
ISSN	1938-5404 ; 0033-7587
ISSN (online)	1938-5404
ISSN	0033-7587
DOI	10.1667/RADE-20-00007
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Article ; Online: Symptom-based early-stage differentiation between SARS-CoV-2 versus other respiratory tract infections-Upper Silesia pilot study.

Mika, Justyna / Tobiasz, Joanna / Zyla, Joanna / Papiez, Anna / Bach, Małgorzata / Werner, Aleksandra / Kozielski, Michał / Kania, Mateusz / Gruca, Aleksandra / Piotrowski, Damian / Sobala-Szczygieł, Barbara / Włostowska, Bożena / Foszner, Paweł / Sikora, Marek / Polanska, Joanna / Jaroszewicz, Jerzy

Scientific reports

2021 Volume 11, Issue 1, Page(s) 13580

Abstract: In the DECODE project, data were collected from 3,114 surveys filled by symptomatic patients RT-qPCR tested for SARS-CoV-2 in a single university centre in March-September 2020. The population demonstrated balanced sex and age with 759 SARS-CoV-2( +) ... ...

Abstract	In the DECODE project, data were collected from 3,114 surveys filled by symptomatic patients RT-qPCR tested for SARS-CoV-2 in a single university centre in March-September 2020. The population demonstrated balanced sex and age with 759 SARS-CoV-2( +) patients. The most discriminative symptoms in SARS-CoV-2( +) patients at early infection stage were loss of taste/smell (OR = 3.33, p < 0.0001), body temperature above 38℃ (OR = 1.67, p < 0.0001), muscle aches (OR = 1.30, p = 0.0242), headache (OR = 1.27, p = 0.0405), cough (OR = 1.26, p = 0.0477). Dyspnea was more often reported among SARS-CoV-2(-) (OR = 0.55, p < 0.0001). Cough and dyspnea were 3.5 times more frequent among SARS-CoV-2(-) (OR = 0.28, p < 0.0001). Co-occurrence of cough, muscle aches, headache, loss of taste/smell (OR = 4.72, p = 0.0015) appeared significant, although co-occurrence of two symptoms only, cough and loss of smell or taste, means OR = 2.49 (p < 0.0001). Temperature > 38℃ with cough was most frequent in men (20%), while loss of taste/smell with cough in women (17%). For younger people, taste/smell impairment is sufficient to characterise infection, whereas in older patients co-occurrence of fever and cough is necessary. The presented study objectifies the single symptoms and interactions significance in COVID-19 diagnoses and demonstrates diverse symptomatology in patient groups.
MeSH term(s)	Academic Medical Centers/statistics & numerical data ; Adolescent ; Adult ; Aged ; Aged, 80 and over ; Ageusia/etiology ; COVID-19/complications ; COVID-19/diagnosis ; COVID-19/epidemiology ; Child ; Child, Preschool ; Cough/etiology ; Diagnosis, Differential ; Dyspnea/etiology ; Female ; Fever/etiology ; Headache/etiology ; Humans ; Infant ; Male ; Middle Aged ; Odds Ratio ; Olfaction Disorders/etiology ; Pilot Projects ; Poland/epidemiology ; Respiratory Tract Infections/complications ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/epidemiology ; Respiratory Tract Infections/microbiology ; SARS-CoV-2 ; Surveys and Questionnaires ; Symptom Assessment/classification ; Symptom Assessment/statistics & numerical data ; Young Adult
Language	English
Publishing date	2021-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-93046-6
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Article ; Online: Low-dose radiation accelerates aging of the T-cell receptor repertoire in CBA/Ca mice.

Candéias, Serge M / Mika, Justyna / Finnon, Paul / Verbiest, Tom / Finnon, Rosemary / Brown, Natalie / Bouffler, Simon / Polanska, Joanna / Badie, Christophe

Cellular and molecular life sciences : CMLS

2017 Volume 74, Issue 23, Page(s) 4339–4351

Abstract: While the biological effects of high-dose-ionizing radiation on human health are well characterized, the consequences of low-dose radiation exposure remain poorly defined, even though they are of major importance for radiological protection. Lymphocytes ... ...

Abstract	While the biological effects of high-dose-ionizing radiation on human health are well characterized, the consequences of low-dose radiation exposure remain poorly defined, even though they are of major importance for radiological protection. Lymphocytes are very radiosensitive, and radiation-induced health effects may result from immune cell loss and/or immune system impairment. To decipher the mechanisms of effects of low doses, we analyzed the modulation of the T-cell receptor gene repertoire in mice exposed to a single low (0.1 Gy) or high (1 Gy) dose of radiation. High-throughput T-cell receptor gene profiling was used to visualize T-lymphocyte dynamics over time in control and irradiated mice. Radiation exposure induces "aging-like" effects on the T-cell receptor gene repertoire, detectable as early as 1 month post-exposure and for at least 6 months. Surprisingly, these effects are more pronounced in animals exposed to 0.1 Gy than to 1 Gy, where partial correction occurs over time. Importantly, we found that low-dose radiation effects are partially due to the hematopoietic stem cell impairment. Collectively, our findings show that acute low-dose radiation exposure specifically results in long-term alterations of the T-lymphocyte repertoire.
MeSH term(s)	Animals ; Cellular Senescence/radiation effects ; Dose-Response Relationship, Radiation ; Gamma Rays ; Gene Expression/immunology ; Gene Expression/radiation effects ; Graft Survival ; Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/cytology ; Hematopoietic Stem Cells/immunology ; Hematopoietic Stem Cells/radiation effects ; Male ; Mice ; Mice, Inbred CBA ; Mice, Inbred NOD ; Protein Isoforms/genetics ; Protein Isoforms/immunology ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/cytology ; T-Lymphocytes/immunology ; T-Lymphocytes/radiation effects ; Transplantation Chimera ; Transplantation, Homologous ; V(D)J Recombination/immunology
Chemical Substances	Protein Isoforms ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2017-12
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1358415-7
ISSN	1420-9071 ; 1420-682X
ISSN (online)	1420-9071
ISSN	1420-682X
DOI	10.1007/s00018-017-2581-2
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Article: Erratum: Cuceu, C., et al. Independent Mechanisms Lead to Genomic Instability in Hodgkin Lymphoma: Microsatellite or Chromosomal Instability.

Cuceu, Corina / Colicchio, Bruno / Jeandidier, Eric / Junker, Steffen / Plassa, François / Shim, Grace / Mika, Justyna / Frenzel, Monika / Al Jawhari, Mustafa / Hempel, William M / Kabacik, Sylwia / Lenain, Aude / Morat, Luc / Girinsky, Theodore / Dieterlen, Alain / Polanska, Joanna / Badie, Christophe / Carde, Patrice / M'Kacher, Radhia

Cancers

2019 Volume 11, Issue 6

Abstract: The authors wish to make the following corrections to this paper [ ... ]. ...

Abstract	The authors wish to make the following corrections to this paper [...].
Language	English
Publishing date	2019-05-30
Publishing country	Switzerland
Document type	Journal Article ; Published Erratum
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers11060757
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