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  1. AU="Cheng-Zhong Zhang"
  2. AU="Song, Jiwu"
  3. AU="Terwilliger, Gordon"
  4. AU="Elhamzaoui, Hamza"
  5. AU="Béganton, Benoît"
  6. AU=Smith Zachary D.
  7. AU="Dotta, Federico"
  8. AU="Palmer, Andre"
  9. AU="Cai, Biao"
  10. AU="Leroux, Michel R"
  11. AU="Thomson, Jaidyn"
  12. AU="Novillo-Del Álamo, Blanca"
  13. AU="Deps, Patrícia D"

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Treffer 1 - 9 von insgesamt 9

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  1. Artikel ; Online: Examining the cooperation between extrachromosomal DNA circles

    Jiahui Zhang / Cheng-Zhong Zhang

    eLife, Vol

    2022  Band 11

    Abstract: In a departure from previous findings, new results suggest that free-floating pieces of DNA which carry additional copies of cancer-driving genes do not tend to cluster or have increased transcription. ...

    Abstract In a departure from previous findings, new results suggest that free-floating pieces of DNA which carry additional copies of cancer-driving genes do not tend to cluster or have increased transcription.
    Schlagwörter extrachromosomal DNA ; oncogenes ; super-resolution imaging ; transcription factors hub ; glioblastoma ; cancer ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Sprache Englisch
    Erscheinungsdatum 2022-12-01T00:00:00Z
    Verlag eLife Sciences Publications Ltd
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: Determination of complete chromosomal haplotypes by bulk DNA sequencing

    Richard W. Tourdot / Gregory J. Brunette / Ricardo A. Pinto / Cheng-Zhong Zhang

    Genome Biology, Vol 22, Iss 1, Pp 1-

    2021  Band 31

    Abstract: Abstract Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes ... ...

    Abstract Abstract Haplotype phase represents the collective genetic variation between homologous chromosomes and is an essential feature of non-haploid genomes. Here we describe a computational strategy to reliably determine complete whole-chromosome haplotypes using a combination of bulk long-range sequencing and Hi-C sequencing. We demonstrate that this strategy can resolve the haplotypes of parental chromosomes in diploid human genomes with high precision (>99%) and completeness (>98%) and assemble the syntenic structure of rearranged chromosomes in aneuploid cancer genomes at base pair level resolution. Our work enables direct interrogation of chromosome-specific alterations and chromatin reorganization using bulk DNA sequencing.
    Schlagwörter Haplotype ; Chromosome rearrangement ; Cancer genomics ; Biology (General) ; QH301-705.5 ; Genetics ; QH426-470
    Sprache Englisch
    Erscheinungsdatum 2021-05-01T00:00:00Z
    Verlag BMC
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  3. Artikel ; Online: Whole chromosome loss and genomic instability in mouse embryos after CRISPR-Cas9 genome editing

    Stamatis Papathanasiou / Styliani Markoulaki / Logan J. Blaine / Mitchell L. Leibowitz / Cheng-Zhong Zhang / Rudolf Jaenisch / David Pellman

    Nature Communications, Vol 12, Iss 1, Pp 1-

    2021  Band 7

    Abstract: A possible undesired outcome of CRISPR-Cas9 germline editing is unwanted karyotype alterations. Here the authors track aberrations through three divisions of embryonic development following Cas9 editing. ...

    Abstract A possible undesired outcome of CRISPR-Cas9 germline editing is unwanted karyotype alterations. Here the authors track aberrations through three divisions of embryonic development following Cas9 editing.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2021-10-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Using whole genome scores to compare three clinical phenotyping methods in complex diseases

    Wenyu Song / Hailiang Huang / Cheng-Zhong Zhang / David W. Bates / Adam Wright

    Scientific Reports, Vol 8, Iss 1, Pp 1-

    2018  Band 10

    Abstract: Abstract Genome-wide association studies depend on accurate ascertainment of patient phenotype. However, phenotyping is difficult, and it is often treated as an afterthought in these studies because of the expense involved. Electronic health records ( ... ...

    Abstract Abstract Genome-wide association studies depend on accurate ascertainment of patient phenotype. However, phenotyping is difficult, and it is often treated as an afterthought in these studies because of the expense involved. Electronic health records (EHRs) may provide higher fidelity phenotypes for genomic research than other sources such as administrative data. We used whole genome association models to evaluate different EHR and administrative data-based phenotyping methods in a cohort of 16,858 Caucasian subjects for type 1 diabetes mellitus, type 2 diabetes mellitus, coronary artery disease and breast cancer. For each disease, we trained and evaluated polygenic models using three different phenotype definitions: phenotypes derived from billing data, the clinical problem list, or a curated phenotyping algorithm. We observed that for these diseases, the curated phenotype outperformed the problem list, and the problem list outperformed administrative billing data. This suggests that using advanced EHR-derived phenotypes can further increase the power of genome-wide association studies.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2018-07-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  5. Artikel ; Online: A preliminary study of markers for human hair follicle melanin stem cell

    Xing-Yu Mei / Zhou-Wei Wu / Cheng-Zhong Zhang / Yue Sun / Wei-Min Shi / Xin Chen

    Chinese Medical Journal, Vol 132, Iss 9, Pp 1117-

    2019  Band 1119

    Schlagwörter Medicine ; R
    Sprache Englisch
    Erscheinungsdatum 2019-05-01T00:00:00Z
    Verlag Wolters Kluwer
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  6. Artikel ; Online: Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma

    Chunyang Bao / Richard W. Tourdot / Gregory J. Brunette / Chip Stewart / Lili Sun / Hideo Baba / Masayuki Watanabe / Agoston T. Agoston / Kunal Jajoo / Jon M. Davison / Katie S. Nason / Gad Getz / Kenneth K. Wang / Yu Imamura / Robert Odze / Adam J. Bass / Matthew D. Stachler / Cheng-Zhong Zhang

    Nature Communications, Vol 14, Iss 1, Pp 1-

    2023  Band 22

    Abstract: Abstract The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy- ... ...

    Abstract Abstract The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett’s esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.
    Schlagwörter Science ; Q
    Thema/Rubrik (Code) 570
    Sprache Englisch
    Erscheinungsdatum 2023-10-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  7. Artikel ; Online: Violin Bridge Mobility Analysis under In-Plane Excitation

    Cheng-Zhong Zhang / Guang-Ming Zhang / Bang-Yan Ye / Li-Dong Liang

    Sensors, Vol 13, Iss 11, Pp 15290-

    2013  Band 15306

    Abstract: The vibration of a violin bridge is a dynamic contact vibration with two interfaces: strings-bridge, and bridge feet-top plate. In this paper, the mobility of an isolated bridge under in-plane excitation is explored using finite element modeling based on ...

    Abstract The vibration of a violin bridge is a dynamic contact vibration with two interfaces: strings-bridge, and bridge feet-top plate. In this paper, the mobility of an isolated bridge under in-plane excitation is explored using finite element modeling based on the contact vibration model. Numerical results show that the dynamic contact stiffness in the two contact interfaces has a great impact on the bridge mobility. A main resonance peak is observed in the frequency range of 2–3 kHz in the frequency response of the isolated bridge when the contact stiffness is smaller than a critical threshold. The main resonance peak frequency is affected by the contact stiffness as well. In order to verify the numerical findings, a novel experimental system is then designed on the basis of a piezoelectric dynamometer for bridge mobility analysis. Experimental results confirm the impact of the dynamic contact stiffness on the bridge mobility.
    Schlagwörter violin bridge ; frequency response ; contact stiffness ; dynamic contact vibration ; dynamometer ; Technology (General) ; T1-995 ; Technology ; T ; DOAJ:Technology (General) ; DOAJ:Technology and Engineering ; Analytical chemistry ; QD71-142 ; Chemistry ; QD1-999 ; Science ; Q ; DOAJ:Analytical Chemistry ; DOAJ:Chemistry
    Thema/Rubrik (Code) 621
    Sprache Englisch
    Erscheinungsdatum 2013-11-01T00:00:00Z
    Verlag MDPI AG
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  8. Artikel ; Online: Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

    Viktor A. Adalsteinsson / Gavin Ha / Samuel S. Freeman / Atish D. Choudhury / Daniel G. Stover / Heather A. Parsons / Gregory Gydush / Sarah C. Reed / Denisse Rotem / Justin Rhoades / Denis Loginov / Dimitri Livitz / Daniel Rosebrock / Ignaty Leshchiner / Jaegil Kim / Chip Stewart / Mara Rosenberg / Joshua M. Francis / Cheng-Zhong Zhang /
    Ofir Cohen / Coyin Oh / Huiming Ding / Paz Polak / Max Lloyd / Sairah Mahmud / Karla Helvie / Margaret S. Merrill / Rebecca A. Santiago / Edward P. O’Connor / Seong H. Jeong / Rachel Leeson / Rachel M. Barry / Joseph F. Kramkowski / Zhenwei Zhang / Laura Polacek / Jens G. Lohr / Molly Schleicher / Emily Lipscomb / Andrea Saltzman / Nelly M. Oliver / Lori Marini / Adrienne G. Waks / Lauren C. Harshman / Sara M. Tolaney / Eliezer M. Van Allen / Eric P. Winer / Nancy U. Lin / Mari Nakabayashi / Mary-Ellen Taplin / Cory M. Johannessen

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Band 13

    Abstract: Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole- ... ...

    Abstract Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-exome sequencing is concordant with metastatic tumour whole-exome sequencing.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2017-11-01T00:00:00Z
    Verlag Nature Portfolio
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  9. Artikel ; Online: Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

    Viktor A. Adalsteinsson / Gavin Ha / Samuel S. Freeman / Atish D. Choudhury / Daniel G. Stover / Heather A. Parsons / Gregory Gydush / Sarah C. Reed / Denisse Rotem / Justin Rhoades / Denis Loginov / Dimitri Livitz / Daniel Rosebrock / Ignaty Leshchiner / Jaegil Kim / Chip Stewart / Mara Rosenberg / Joshua M. Francis / Cheng-Zhong Zhang /
    Ofir Cohen / Coyin Oh / Huiming Ding / Paz Polak / Max Lloyd / Sairah Mahmud / Karla Helvie / Margaret S. Merrill / Rebecca A. Santiago / Edward P. O’Connor / Seong H. Jeong / Rachel Leeson / Rachel M. Barry / Joseph F. Kramkowski / Zhenwei Zhang / Laura Polacek / Jens G. Lohr / Molly Schleicher / Emily Lipscomb / Andrea Saltzman / Nelly M. Oliver / Lori Marini / Adrienne G. Waks / Lauren C. Harshman / Sara M. Tolaney / Eliezer M. Van Allen / Eric P. Winer / Nancy U. Lin / Mari Nakabayashi / Mary-Ellen Taplin / Cory M. Johannessen / Levi A. Garraway / Todd R. Golub / Jesse S. Boehm / Nikhil Wagle / Gad Getz / J. Christopher Love / Matthew Meyerson

    Nature Communications, Vol 8, Iss 1, Pp 1-

    2017  Band 13

    Abstract: Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole- ... ...

    Abstract Identifying the mutational landscape of tumours from cell-free DNA in the blood could help diagnostics in cancer. Here, the authors present ichorCNA, software that quantifies tumour content in cell free DNA, and they demonstrate that cell-free DNA whole-exome sequencing is concordant with metastatic tumour whole-exome sequencing.
    Schlagwörter Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2017-11-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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