Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

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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 ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

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 ...

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 ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

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 ...

Motivated by the transfer of proofs between proof systems, and in particular from first order automated theorem provers (ATPs) to interactive theorem provers (ITPs), we specify an extension of the TPTP derivation text format to describe proofs in first-ord ...

We study the proof theory and algorithms for orthologic, a logical system based on ortholattices, which have shown practical relevance in simplification and normalization of verification conditions. Ortholattices weaken Boolean algebras while having polyno ...

Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...

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 ...

We prove the non-planarity of a family of 3-regular graphs constructed from the solutions to the Markoff equation x2 + y2 + z2 = xyz modulo prime numbers greater than 7. The proof uses Euler characteristic and an enumeration of the short cycles in these gr ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Zebrafish have the capacity to fully regenerate the heart after an injury, which lies in sharp contrast to the irreversible loss of cardiomyocytes after a myocardial infarction in humans. Transcriptomics analysis has contributed to dissect underlying signa ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

We present LISA, a proof system and proof assistant for constructing proofs in schematic first-order logic and axiomatic set theory. The logical kernel of the system is a proof checker for first-order logic with equality and schematic predicate and fun ...

A hash proof system (HPS) is a form of implicit proof of membership to a language. Out of the very few existing post-quantum HPS, most are based on languages of ciphertexts of code-based or lattice-based cryptosystems and inherently suffer from a gap cause ...

Acinetobacter baumannii is a dangerous nosocomial pathogen, especially due to its ability to rapidly acquire new genetic traits, including antibiotic resistance genes (ARG). In A. baumannii, natural competence for transformation, one of the primary modes o ...

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Chattez avec Graph Search

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

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

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

SC-TPTP: An Extension of the TPTP Derivation Format for Sequent-Based Calculus

Orthologic with Axioms

Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Variant-specific pathophysiological mechanisms of AFF3 differently influence transcriptome profiles

Non-planarity of Markoff graphs mod p

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Statistical learning quantifies transposable element-mediated cis-regulation

Transcriptomic data meta-analysis reveals common and injury model specific gene expression changes in the regenerating zebrafish heart

Chromatin modules and their implication in genomic organization and gene regulation

LISA – A Modern Proof System

A Gapless Post-quantum Hash Proof System in the Hamming Metric

DNA modifications impact natural transformation of Acinetobacter baumannii