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Whereas the relationship between criticality of gene regulatory networks (GRNs) and dynamics of GRNs at a single cell level has been vigorously studied, the relationship between the criticality of GRNs and system properties at a higher…
CRISPR-based genome editing has revolutionized biotechnology, yet optimizing guide RNA (gRNA) design for efficiency and safety remains a critical challenge. Recent advances (2020--2025, updated to reflect current year if needed) demonstrate…
Lung transplantation remains the only viable treatment option for the majority of patients with advanced lung diseases. However, 5-year post-transplant survival rates remain low primarily secondary to chronic rejection. Novel insights from…
Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is…
Summary: Long non-coding RNAs (lncRNAs) exert their functions by cooperating with other molecules including proteins and DNA. Triplexes, formed through the interaction between a single-stranded RNA (ssRNA) and a double-stranded DNA (dsDNA),…
By analyzing the spacing of genes on chromosomes, we find that transcriptional and RNA-processing regulatory sequences outside coding regions leave footprints on the distribution of intergenic distances. Using analogies between genes on…
Generative AI acts as a disruptive technological shock to evaluative organizations. In academic peer review, it enters both sides of the market: authors use AI to polish submissions, and reviewers use it to generate plausible reports…
This proceeding is based on arXiv:1105.0591 [hep-th] where we consider breaking of supersymmetry in intersecting D-brane configurations by slight deviation of the angles from their supersymmetric values. We compute the masses generated by…
Deep neural networks (DNNs) show promise in image-based medical diagnosis, but cannot be fully trusted since their performance can be severely degraded by dataset shifts to which human perception remains invariant. If we can better…
The rupture of double-stranded DNA under stress is a key process in biophysics and nanotechnology. In this article we consider the shear-induced rupture of short DNA duplexes, a system that has been given new importance by recently designed…
In recent years, the surge in retractions has been accompanied by numerous papers receiving comments that raise concerns about their reliability. The prevalence of problematic papers undermines the reliability of scientific research and…
Spectroscopic measurements can show distorted spectral shapes arising from a mixture of absorbing and scattering contributions. These distortions (or baselines) often manifest themselves as non-constant offsets or low-frequency…
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput…
Existing benchmarks for Deep Research Agents (DRAs) treat report generation as a single-shot writing task, which fundamentally diverges from how human researchers iteratively draft and revise reports via self-reflection or peer feedback.…
We study whether state-of-the-art AI coding agents, given the same data and research question, produce the same empirical results. Deploying 150 autonomous Claude Code agents to independently test six hypotheses about market quality trends…
Even under constant external conditions, the expression levels of genes fluctuate. Much emphasis has been placed on the components of this noise that are due to randomness in transcription and translation; here we analyze the role of noise…
Machine common sense remains a broad, potentially unbounded problem in artificial intelligence (AI). There is a wide range of strategies that can be employed to make progress on this challenge. This article deals with the aspects of…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Distant supervision (DS) is a well established technique for creating large-scale datasets for relation extraction (RE) without using human annotations. However, research in DS-RE has been mostly limited to the English language.…
The emerging field of epigenetics has recently unveiled a dynamic landscape in which gene expression is not determined solely by genetic sequences but also by intricate regulatory mechanisms. This review examines the interactions between…