Results 51 to 60 of about 215,700 (227)

DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis [PDF]

Genes, 2019
Abstract Background It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (Chromosome Conformation Capture) and its derived methods are now widely applied to investigate genome organizations and gene regulation ...
Hong, Ping, Jiang, Hao, Xu, Weize, Lin, Da, Xu, Qian, Cao, Gang, Li, Guoliang   +6 more
openaire   +3 more sources

HiGlass: web-based visual exploration and analysis of genome interaction maps

Genome Biology, 2018
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types ...
Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas, Chuck McCallum, Kasper Dinkla, Hendrik Strobelt, Jacob M. Luber, Scott B. Ouellette, Alaleh Azhir, Nikhil Kumar, Jeewon Hwang, Soohyun Lee, Burak H. Alver, Hanspeter Pfister, Leonid A. Mirny, Peter J. Park, Nils Gehlenborg   +16 more
doaj   +1 more source

Rich chromatin structure prediction from Hi-C data [PDF]

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015
ABSTRACT Recent studies involving the 3-dimensional conformation of chromatin have revealed the important role it has to play in different processes within the cell. These studies have also led to the discovery of densely interacting segments of the chromosome, called topologically associating domains.
Laraib Malik, Rob Patro
openaire   +2 more sources

Mapping Childhood Cancer Care Services in Oceania: Methodological Lessons From the SIOP Global Mapping Programme

Pediatric Blood &Cancer, EarlyView.
ABSTRACT The International Paediatric Oncology Society Global Mapping Programme aims to collect data on global paediatric oncology services by continent, with Africa and Latin America completed. This study reports on the methodology and lessons learned for Oceania, a unique continent with resource disparity across countries, multiple small island ...
Trisha Soosay Raj, Christy Noble, Amy Gray, Daniel C. Moreira, Jennifer Lowe, Maite Gorostegui, Gwenda Anga, Andrew Soma, Milena Lay Dos Santos, Siobhan Cross, Erin Luttrell, Michael Sullivan, Julie Cayrol, Julia Challinor, Neil Ranasinghe, Jordana McLoone, Claire E. Wakefield   +16 more
wiley   +1 more source

GILoop: Robust chromatin loop calling across multiple sequencing depths on Hi-C data

iScience, 2022
Summary: Graph and image are two common representations of Hi-C cis-contact maps. Existing computational tools have only adopted Hi-C data modeled as unitary data structures but neglected the potential advantages of synergizing the information of ...
Fuzhou Wang, Tingxiao Gao, Jiecong Lin, Zetian Zheng, Lei Huang, Muhammad Toseef, Xiangtao Li, Ka-Chun Wong   +7 more
doaj   +1 more source

Valosin‐containing protein counteracts ATP‐driven dissolution of FUS condensates through its ATPase activity in vitro

FEBS Letters, EarlyView.
Biomolecular condensates formed by fused in sarcoma (FUS) are dissolved by high ATP concentrations yet persist in cells. Using a reconstituted system, we demonstrate that valosin‐containing protein (VCP), an AAA+ ATPase, counteracts ATP‐driven dissolution of FUS condensates through its D2 ATPase activity.
Hitomi Kimura, Shin‐ichi Tate, Kyota Yasuda   +2 more
wiley   +1 more source

AscF in the mycobacterial CIII–CIV supercomplex lacks metal and nucleotide binding but links malate oxidation to respiration

FEBS Letters, EarlyView.
The mycobacterial CIII‐CIV respiratory supercomplex is an obligate assembly, encompassing several subunits of unknown functions. We have characterized the intracellular subunit AscF, and show that it is unlikely to be a sensor for metals or nucleotides, but is required for growth on nonfermentable energy sources, and likely works as an adapter for ...
Eni Rile, Riccardo Diamanti, Daniel Lundin, Soni Sharma, Robin Lissner, Coenraad P. Kuil, Martin Högbom, Dirk Bald, Dan Sjöstrand   +8 more
wiley   +1 more source

Algorithmic considerations when analysing capture Hi-C data [version 2; peer review: 2 approved]

Wellcome Open Research, 2022
Chromosome conformation capture methodologies have provided insight into the effect of 3D genomic architecture on gene regulation. Capture Hi-C (CHi-C) is a recent extension of Hi-C that improves the effective resolution of chromatin interactions by ...
Linden Disney-Hogg, Richard Houlston, Ben Kinnersley   +2 more
doaj   +1 more source

SnapHiC2: A computationally efficient loop caller for single cell Hi-C data

Computational and Structural Biotechnology Journal, 2022
Single cell Hi-C (scHi-C) technologies enable the study of chromatin spatial organization directly from complex tissues at single cell resolution.
Xiaoqi Li, Lindsay Lee, Armen Abnousi, Miao Yu, Weifang Liu, Le Huang, Yun Li, Ming Hu   +7 more
doaj   +1 more source

Single‐cell DNA methylation profiling: Technologies, computation, and applications in precision oncology

Molecular Oncology, EarlyView.
Single‐cell DNA methylation (scDNAme) profiling maps epimutational clonal evolution, revealing mechanisms of malignancy and therapeutic resistance across diverse cancer types. By providing a high‐resolution landscape of intratumoral heterogeneity, these technologies empower precise patient stratification, guide the development of enhanced ...
Ik Soo Kim
wiley   +1 more source