Genome Biology

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Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains
Genome Biology - Tập 21 - Trang 1-19 - 2020
Elissavet Kentepozidou, Sarah J. Aitken, Christine Feig, Klara Stefflova, Ximena Ibarra-Soria, Duncan T. Odom, Maša Roller, Paul Flicek
CTCF binding contributes to the establishment of a higher-order genome structure by demarcating the boundaries of large-scale topologically associating domains (TADs). However, despite the importance and conservation of TADs, the role of CTCF binding in their evolution and stability remains elusive. We carry out an experimental and computational study that exploits the natural genetic variation ac...... hiện toàn bộ
Predicting the sites of metastases
Genome Biology - Tập 6 - Trang 1-4 - 2005
Brian Z Ring, Douglas T Ross
Transplantation of human breast cancer cells into immunodeficient mice together with gene-expression microarray studies has recently identified genes implicated in the tissue tropism of breast-cancer metastasis. Such signatures of site-specific metastatic capabilities might allow the targeting of therapy to likely sites of metastasis.
Author Correction: Towards accurate and reliable resolution of structural variants for clinical diagnosis
Genome Biology - Tập 23 - Trang 1-2 - 2022
Zhichao Liu, Ruth Roberts, Timothy R. Mercer, Joshua Xu, Fritz J. Sedlazeck, Weida Tong
An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding
Genome Biology - Tập 22 - Trang 1-25 - 2021
Divyanshi Srivastava, Begüm Aydin, Esteban O. Mazzoni, Shaun Mahony
Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor’s DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with transcription factor binding in a given cell type have been well characterized. For instance, the binding sites for a majority of transcription factors display concurre...... hiện toàn bộ
Integrating whole transcriptome sequence data and public databases for analysis of somatic mutations in tumors
Genome Biology - Tập 12 - Trang 1-27 - 2011
Amin A Momin, Brian P James, Thomas C Motter, Humam N Kadara, Garth Powis, Ignacio I Wistuba
France failing young scientists
Genome Biology - Tập 4 - Trang 1-3 - 2003
Jane Burgermeister
Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans
Genome Biology - - 2006
Helga David, Gerald Hofmann, Ana Paula Oliveira, Hanne Jarmer, Jens Nielsen
Aspergillus nidulans (the asexual form of Emericella nidulans) is a model organism for aspergilli, which are an important group of filamentous fungi that encompasses human and plant pathogens as well as industrial cell factories. Aspergilli have a highly diversified metabolism and, because of their medical, agricultural and biotechnological importance, it would be valuable to have an understanding...... hiện toàn bộ
deconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution
Genome Biology - Tập 17 - Trang 1-11 - 2016
Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Barry S. Taylor, Charles Swanton
Analysis of somatic mutations provides insight into the mutational processes that have shaped the cancer genome, but such analysis currently requires large cohorts. We develop deconstructSigs, which allows the identification of mutational signatures within a single tumor sample. Application of deconstructSigs identifies samples with DNA repair deficiencies and reveals distinct and dynamic mutation...... hiện toàn bộ
Insights from the 2018 Biology of Genomes meeting
Genome Biology - Tập 19 Số 1 - Trang 1-3 - 2018
Oak, Ninad, Plon, Sharon E.
A report on the Cold Spring Harbor Laboratory 31st annual meeting on the Biology of Genomes, held at Cold Spring Harbor, New York, USA, 8–12 May, 2018. The 2018 Biology of Genomes meeting at Cold Spring Harbor Laboratories covered a wide range of topics with research relevant to many aspects of genomics. Here we highlight two areas of research where multiple talks provided new insights.
Systemic analysis of the response of Aspergillus nigerto ambient pH
Genome Biology - Tập 10 - Trang 1-14 - 2009
Mikael R Andersen, Linda Lehmann, Jens Nielsen
The filamentous fungus Aspergillus niger is an exceptionally efficient producer of organic acids, which is one of the reasons for its relevance to industrial processes and commercial importance. While it is known that the mechanisms regulating this production are tied to the levels of ambient pH, the reasons and mechanisms for this are poorly understood. To cast light on the connection between ext...... hiện toàn bộ
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