Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

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Deep learning has shown remarkable potential for industrial applications, particularly in predictive maintenance and condition monitoring. A key challenge in this domain is prognostics, specifically predicting the Remaining Useful Life (RUL) of assets - a ...

The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learni ...

Cyclic peptides are attractive for drug discovery due to their excellent binding properties and the potential to cross cell membranes. However, by far not all cyclic peptides are cell permeable, and measuring or predicting their membrane permeability is no ...

Recordings of the physiological history of cells provide insights into biological processes, yet obtaining such recordings is a challenge. To address this, we introduce a method to record transient cellular events for later analysis. We designed proteins t ...

This thesis focuses on understanding and improving the reasoning capabilities of neural networks. It develops theoretical results and empirical analyses to uncover reasoning potential and limitations, leveraging these insights to guide the design of improv ...

Semi-supervised semantic segmentation methods leverage unlabeled data by pseudo-labeling them. Thus the success of these methods hinges on the reliability of the pseudo-labels. Existing methods mostly choose high-confidence pixels in an effort to avoid err ...

The advent of immunotherapy, such as immune checkpoint blockade (ICB) and adoptive transfer of cytotoxic lymphocytes, has transformed the clinical care of cancer. However, a significant proportion of patients are resistant to immunotherapy or experience re ...

Machine learning models (e.g., neural networks) achieve high accuracy in wind power forecasting, but they are usually regarded as black boxes that lack interpretability. To address this issue, the paper proposes a glass-box model that combines high accurac ...

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 ...

A search is presented for the pair production of new heavy resonances, each decaying into a top quark (t) or antiquark and a gluon (g). The analysis uses data recorded with the CMS detector from proton-proton collisions at a center-of-mass energy of 13 TeV ...

Heterochromatin loss and genetic instability enhance cancer progression by favoring clonal diversity, yet uncontrolled replicative stress leads to mitotic catastrophe and inflammatory responses that promote immune rejection. KRAB domain-containing zinc fin ...

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

The upcoming Square Kilometre Array Observatory will produce images of neutral hydrogen distribution during the epoch of reionization by observing the corresponding 21-cm signal. However, the 21-cm signal will be subject to instrumental limitations such as ...

The synthesis of complex sugars is a key aspect of microbial biology. Cyclic beta-1,2-glucan (C beta G) is a circular polysaccharide critical for host interactions of many bacteria, including major pathogens of humans (Brucella) and plants (Agrobacterium). ...

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

The capabilities of deep learning systems have advanced much faster than our ability to understand them. Whilst the gains from deep neural networks (DNNs) are significant, they are accompanied by a growing risk and gravity of a bad outcome. This is troubli ...

Despite the widespread empirical success of ResNet, the generalization properties of deep ResNet are rarely explored beyond the lazy training regime. In this work, we investigate scaled ResNet in the limit of infinitely deep and wide neural networks, of wh ...

Infectious agents contribute significantly to the global burden of diseases through both acute infection and their chronic sequelae. We leveraged the UK Biobank to identify genetic loci that influence humoral immune response to multiple infections. From 45 ...

Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

G-protein-coupled receptors (GPCRs) are key regulators of human physiology and are the targets of many small-molecule research compounds and therapeutic drugs. While most of these ligands bind to their target GPCR with high affinity, selectivity is often l ...

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Chattez avec Graph Search

Overcoming Distribution Shifts and Imbalance Challenges in Representation Learning for Deep Regression Models

Computational drug development for membrane protein targets

Bulk measurement of membrane permeability for random cyclic peptides in living cells to guide drug development

Recording physiological history of cells with chemical labeling

Learning to Reason with Neural Networks: Principles and Methods

Weighting Pseudo-labels via High-Activation Feature Index Similarity and Object Detection for Semi-supervised Segmentation

Exploration and modulation of mechanical cues for enhanced cancer immunotherapy

Explainable modeling for wind power forecasting: A Glass-Box model with high accuracy

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

Search for Pair Production of Heavy Particles Decaying to a Top Quark and a Gluon in the Lepton Plus Jets Final State in Proton-proton Collisions at √s=13 Tev

A Cluster of Evolutionarily Recent KRAB Zinc Finger Proteins Protects Cancer Cells from Replicative Stress–Induced Inflammation

Microsecond time-resolved cryo-electron microscopy

Deep learning approach for identification of H II regions during reionization in 21-cm observations - II. Foreground contamination

Structure-function analysis of the cyclic β-1,2-glucan synthase from Agrobacterium tumefaciens

Structural heterogeneity of the ion and lipid channel TMEM16F

Safe Deep Neural Networks

Generalization of Scaled Deep ResNets in the Mean-Field Regime

A common NFKB1 variant detected through antibody analysis in UK Biobank predicts risk of infection and allergy

HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology

Antibodies expand the scope of angiotensin receptor pharmacology