13 papers · ranked by Valyu relevance
Mario Catalano, Gerardo Pepe, Gabriele Ausiello, Romina Appierdo + 4 more
Computational predictions are essential to characterize the RNA–protein interaction landscape, yet a persistent gap between benchmark performance and practical utility suggests that current models have limited generalization capabilities. To address this issue, we present CORAL (Cross-attention for RNA-protein…
Khalid K. Alam, Kwaku D. Tawiah, Matthew F. Lichte, David Porciani + 1 more
RNA-RNA assembly governs key biological processes and is a powerful tool for engineering synthetic genetic circuits. Characterizing RNA assembly in living cells often involves monitoring fluorescent reporter proteins, which are at best indirect measures of underlying RNA-RNA hybridization events and are subject to…
Zida Li, Luoquan Li, Meixiang Liao, Liqun He + 1 more
Removing volumes from droplets is a challenging but critical step in many droplet-based applications. Geometry-mediated droplet splitting has the potential to reliably divide droplets and thus facilitate the implementation of this step. In this paper, we report the design of multi-furcating microfluidic channels for…
Florian Privé
A few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them sub-optimal. Here we develop an optimal solution for this problem using dynamic programming. This is now…
Shunit Olszakier, Wessal Hussein, Ronit Heinrich, Michael Andreyanov + 4 more
We assessed the feasibility of using stop-codons as means to obtain polycistronic expression in eukaryotic cells. We show robust bicistronic expression of different open reading frames (ORFs), when these are cloned in-sequence and simply separated by stop codons (in-or out-of-frame), in heterologous expression systems…
Roman Joeres, David B. Blumenthal, Olga V. Kalinina
Information Leakage is an increasing problem in machine learning research. It is a common practice to report models with benchmarks, comparing them to the state-of-the-art performance on the test splits of datasets. If two or more dataset splits contain identical or highly similar samples, a model risks simply…
Haojiang Luan, Alexander Kuzin, Ward F. Odenwald, Benjamin H. White
Genetic methods for targeting small numbers of neurons of a specific type are critical for mapping the brain circuits underlying behavior. Existing methods can provide exquisite targeting precision in favorable cases, but for many cases alternative techniques will be required. Here, we introduce a new step-wise…
Taja Železnik Ramuta, Jaka Snoj, Tina Kos, Ajasja Ljubetič + 2 more
Strategies for detecting and controlling protein interactions play a critical role in gaining insight into molecular mechanisms of biological processes and for the control of cellular processes. Conditional protein reconstitution allows control of the selected protein function based on the proximity, defined by the…
Mamoru Ishii, Tomoaki Kinjo, Yohei Kondo, Kenta Terai + 3 more
Multiplexed live cell-labeling technologies are essential tools for investigating complex biological systems, yet existing approaches face limitations in achieving reliable discrimination of multiple cell populations. Here, we present color and intensity modulation with split fluorescent proteins for cell labeling…
Suraj Makhija, David Brown, Struan Bourke, Yina Wang + 4 more
Recent advances in genome engineering have expanded our capabilities to study proteins in their natural states. In particular, the ease and scalability of knocking-in small peptide tags has enabled high throughput tagging and analysis of endogenous proteins. To improve enrichment capacities and expand the functionality…
Wei-Hong Yeo, Cheng Sun, Hao F. Zhang
The dual-wedge prism (DWP)-based spectroscopic single-molecule localization microscopy (sSMLM) system offers improved localization precision and adjustable spectral or localization performance, but its nonlinear spectral dispersion presents a challenge. A systematic method can help understand the challenges and…
Mert Özkan, Viola Störmer
Spatial attention enables us to select regions of space and prioritize visual processing at the attended locations. Previous research has shown that spatial attention can be flexibly tuned to broader or narrower regions in space, and in some cases be split amongst multiple locations. Here, we investigate how…
N. Hümpfer, Z. Marin, A. Zehtabian, K. Bruckmann + 4 more
After separation of duplicated genetic material, animal cells divide by cytokinesis. This process involves several simultaneous and successive steps of molecular reorganization at cell membrane, cortex and the spindle apparatus as the cleavage furrow ingresses and the spindle is transformed into the intercellular…