Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains

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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 ...

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

Scaffold-based protein libraries are designed to be both diverse and rich in functional/folded proteins. However, introducing an extended diversity while preserving stability of the initial scaffold remains a challenge. Here we developed an original approa ...

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

Understanding how biological matter takes its shape is instrumental to biology, bioengineering, medicine, and bioinspired engineering. Gaining information on the principles of morphogenesis could enable clinicians to correct developmental abnormalities, ev ...

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

Central nervous system organogenesis is a complex process that obeys precise architectural rules. The impact that nervous system architecture may have on its functionality remains, however, relatively unexplored. To clarify this problem, we analyze the dev ...

Proteins control nearly every facet of life on a molecular level. Proteins are formed from linear strings of amino acids, which fold into three-dimensional structures that can enact functions. Evolution has created highly efficient proteins in diverse fold ...

In vertebrate embryos, the elongating body axis is patterned via the sequential and rhyth-mic production of segments from a posterior unsegmented tissue called the presomitic mesoderm (PSM). This process is controlled by a population of cellular oscillator ...

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 ...

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains

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Statistical learning quantifies transposable element-mediated cis-regulation

Protein target highlights in CASP15: Analysis of models by structure providers

Design of an artificial phage-display library based on a new scaffold improved for average stability of the randomized proteins

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Development of a Robotic Microsurgeon for Embryonic Research

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Puckered and JNK signaling in pioneer neurons coordinates the motor activity of the Drosophila embryo

De novo designed proteins: a study in engineering novel folds and functions

How are cells instructed to form somite boundaries by the zebrafish segmentation clock?

Chromatin modules and their implication in genomic organization and gene regulation

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy