14 papers · ranked by Valyu relevance
Yannick Mahlich, Chengsheng Zhu, Henri Chung, Pavan K. Velaga + 4 more
Determining the repertoire of a microbe’s molecular functions is a central question in microbial biology. Modern techniques achieve this goal by comparing microbial genetic material against reference databases of functionally annotated genes/proteins or known taxonomic markers such as 16S rRNA. Here we describe a novel…
Marlena Duda, Jiayu Chen, Aysenil Belger, Judith Ford + 6 more
The precise relationship between brain structure and function has been investigated through a multitude of lenses, but one detail that is held constant across most neuroimaging studies in this space is the identification of a singular structural basis set of the brain, upon which functional activation signals can be…
Ingrid Billault-Chaumartin, Olivia Muriel, Laetitia Michon, Sophie G Martin
Spatial accumulation of secretory vesicles underlies various cellular processes, such as neurotransmitter release at neuronal synapses [1], hyphal steering in filamentous fungi [2, 3], and local cell wall digestion preceding the fusion of yeast gametes [4]. Secretory vesicles transported on actin filaments by myosin V…
Gabriele Picco, Elisabeth D Chen, Luz Garcia Alonso, Fiona M Behan + 16 more
Many gene fusions have been reported in tumours and for most their role remains unknown. As fusions can be used clinically for diagnostic and prognostic purposes, and are targets for treatment, it is crucial to assess their functional implications in cancer. To investigate the role of fusions in tumor cell fitness, we…
Charlie Murphy, Olivier Elemento
The discovery of novel gene fusions in tumor samples has rapidly accelerated with the rise of next-generation sequencing. A growing number of tools enable discovery of gene fusions from RNA-seq data. However it is likely that not all gene fusions are driving tumors. Assessing the potential functional consequences of a…
Lei Wu, Marlena Duda, Armin Iraji, Vince D. Calhoun
The integration of multimodal MRI images, including functional MRI (fMRI) and diffusion MRI (dMRI), depicts a key advancement in neuroimaging, since it offers a more comprehensive and better understanding of brain function and connections. FMRI captures brain functional activity while dMRI reveals structural…
Clari Valansi, David Moi, Evgenia Leikina, Elena Matveev + 5 more
Cell-cell fusion is inherent to any form of sexual reproduction. Loss of HAPLESS 2/GENERATIVE CELL SPECIFIC 1 (HAP2/GCS1) proteins results in gamete fusion failure in different organisms but their exact role is unclear. Here we show that Arabidopsis HAP2/GCS1 expression in mammalian cells is sufficient to promote…
Olivier Dennler, Elisa Chenel, François Coste, Samuel Blanquart + 2 more
FUSE-PhyloTree is a phylogenomic analysis software for identifying local sequence conservation associated with the different functions of a multi-functional (e.g., paralogous or multi-domain) protein family. FUSE-PhyloTree introduces an original approach that combines advanced sequence analysis with phylogenetic…
Cuyler Luck, Kyle A. Jacobs, Ross A. Okimoto
Rearrangements between genes can yield neomorphic fusions that drive oncogenesis. Fusion oncogenes are made up of fractional segments of the partner genes that comprise them, with each partner potentially contributing some of its own function to the nascent fusion oncoprotein. Clinically, fusion oncoproteins driving…
Nicolas G. Brukman, Kohdai P. Nakajima, Clari Valansi, Kateryna Flyak + 3 more
Mammalian sperm-egg adhesion depends on the trans-interaction between the sperm-specific type I glycoprotein IZUMO1 and its oocyte-specific GPI-anchored receptor JUNO. However, the mechanisms and proteins (fusogens) which mediate the following step of gamete fusion remain unknown. Using live imaging and content mixing…
Roozbeh Dehghannasiri, Donald Eric Freeman, Milos Jordanski, Gillian L. Hsieh + 3 more
The extent to which gene fusions function as drivers of cancer remains a critical open question. Current algorithms do not sufficiently identify false-positive fusions arising during library preparation, sequencing, and alignment. Here, we introduce a new algorithm, DEEPEST, that uses statistical modeling to minimize…
KuaiKuai Duan, Rogers F. Silva, Md Abdur Rahaman, Zening Fu + 5 more
Multimodal data collected by international and national biobanking efforts have distinct scales and model orders and provide unique and complementary insights into disease mechanisms. We propose a novel, flexible and efficient data fusion approach—aNy-way independent component analysis (aNy-way ICA). aNy-way ICA fuses…
Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu + 3 more
Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that…
Saadiah Arshed, Murray P. Cox, Ross E. Beever, Stephanie L. Parkes + 3 more
Vegetative incompatibility is a fungal allorecognition system characterised by the inability of genetically distinct conspecific fungal strains to form a viable heterokaryon, and is controlled by multiple polymorphic loci termed vic (vegetative incompatibility) or het (heterokaryon incompatibility). We have genetically…