A transcript perspective on evolution

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The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

We study the hitting probabilities of the solution to a system of d stochastic heat equations with additive noise subject to Dirichlet boundary conditions. We show that for any bounded Borel set with positive (d-6)\documentclass[12pt]{minimal} \usepackage{ ...

In this article, we propose a dynamical system to avoid obstacles which are star shaped and simultaneously converge to a goal. The convergence is almost-global in a domain and the stationary points are identified explicitly. Our approach is based on the id ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Decision-making permeates every aspect of human and societal development, from individuals' daily choices to the complex decisions made by communities and institutions. Central to effective decision-making is the discipline of optimization, which seeks th ...

When two objects slide against each other, wear and friction occur at their interface. The accumulation of wear forms what is commonly referred to as a ``third-body''. Understanding third-body evolution has significant applications in industry, where contr ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

Image information about the state of a building after an earthquake, which can be collected without endangering the post-earthquake reconnaissance activities, can be used to reduce uncertainties in response predictions for future seismic events. This paper ...

Let F be a family of n pairwise intersecting circles in the plane. We show that the number of lenses, that is convex digons, in the arrangement induced by F is at most 2n - 2. This bound is tight. Furthermore, if no two circles in F touch, then the geometr ...

Realand imaginary -time quantum state evolutions are crucial in physics and chemistry for exploring quantum dynamics, preparing ground states, and computing thermodynamic observables. On near -term devices, variational quantum time evolution is a promising ...

Background: We previously described the KINSSHIP syndrome, an autosomal dominant disorder associated with intellectual disability (ID), mesomelic dysplasia and horseshoe kidney,caused by de novo variants in the degron of AFF3. Mouse knock-ins and overexpre ...

Given a sequence of functions

f_1,\ldots,f_n

with

f_i:\mathcal{D}\mapsto \mathbb{R}

, finite-sum minimization seeks a point

{x}^\star \in \mathcal{D}

minimizing

\sum_{j=1}^nf_j(x)/n

. In this work, we propose a key twist into the finite-sum minimizat ...

Diffusion-based generative methods have proven effective in modeling trajectories with offline datasets. However, they often face computational challenges and can falter in generalization, especially in capturing temporal abstractions for long- horizon tas ...

Conventional techniques for purifying macromolecular conjugates often require complex and costly installments that are inaccessible to most laboratories. In this work, we develop a one-step micropreparative method based on a trilayered polyacrylamide gel e ...

We study the drainage of a viscous liquid film coating the outside of a solid horizontal cylinder, where gravity acts vertically. We focus on the limit of large Ohnesorge numbers Oh, where inertia is negligible compared to viscous effects. We first study t ...

In algorithms for solving optimization problems constrained to a smooth manifold, retractions are a well-established tool to ensure that the iterates stay on the manifold. More recently, it has been demonstrated that retractions are a useful concept for ot ...

A transcript perspective on evolution

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Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

The role of LRRK2 in lung adenocarcinoma

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Hitting with Probability One for Stochastic Heat Equations with Additive Noise

Dynamical system approach to navigation around obstacles

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Reliable data-driven decision-making through optimal transport

Modeling friction and wear using an adaptive discrete-continuum coupling

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Reducing uncertainties in response predictions of earthquake-damaged masonry buildings using data from image-based inspection

A Note on Lenses in Arrangements of Pairwise Intersecting Circles in the Plane

Variational quantum time evolution without the quantum geometric tensor

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Efficient Continual Finite-Sum Minimization

SIMPLE HIERARCHICAL PLANNING WITH DIFFUSION

Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates

Stability of a liquid layer draining around a horizontal cylinder: Interplay of capillary and gravity forces

From low-rank retractions to dynamical low-rank approximation and back