Publications related to Nanopore sensing of single molecules application to RNAP-DNA complexes, fabrication of graphene-nanopore devices and translocation algorithm analysis

Related publications (33)

Abstract 4588: Cell states and resistance in colorectal cancer: What can we learn from patient-derived organoids?

Colorectal cancer (CRC) is among the three most commonly diagnosed cancers and one of the major causes of cancer-related morbidity and mortality. Despite the discovery of several predictive biomarkers, the 5-year survival rate for metastatic CRC is 15%. A ...

American Association for Cancer Research (AACR)2025

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

Dariia Gudkova, Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Hüseyin Baris Atakan, Daniel Alpern, Mustafa Demir

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 ...

Springer2024

Stimulus-responsive assembly of nonviral nucleocapsids

Angela Steinauer

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

Nature Portfolio2024

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

Maria Brbic

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 ...

Nature Publishing Group2024

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Tamar Kohn, Xavier Fernandez Cassi

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

2024

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Christina Ernst

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 ...

Nature Portfolio2024

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

Nils Rädecker

Objectives The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat str ...

BMC2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates

Ardemis Anoush Boghossian, Yahya Rabbani, Shang-Jung Wu, Vitalijs Zubkovs, Sayyed Hashem Sajjadi

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 ...

2024

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

Yanheng Guo

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

EPFL2024

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Alex Russell Lederer

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

EPFL2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger, Sophia Kathryn Johnson

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

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

Cyril David Son-Tuyên Pulver

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 ...

EPFL2024

Nongenetic evolution of the tumor: from challenges to new therapeutic opportunities

Elisa Oricchio

The ability of cancer cells to change and adapt poses a critical challenge to identifying curative solutions. Tumor evolution has been extensively studied from a genetic perspective, to guide clinicians in selecting the most appropriate therapeutic option ...

WILEY2024

Measuring electrical properties in semiconductor devices by pixelated STEM and off-axis electron holography (or convergent beams vs. plane waves)

Victor Carle Adrien Boureau

We demonstrate the use of both pixelated differential phase contrast (DPC) scanning transmission electron microscopy (STEM) and off-axis electron holography (EH) for the measurement of electric fields and assess the advantages and limitations of each techn ...

Pergamon-Elsevier Science Ltd2024

Resonant Tip-Enhanced Raman Spectroscopy of a Single-Molecule Kondo System

Jiri Dolezal

Tip-enhanced Raman spectroscopy (TERS) under ultrahigh vacuum and cryogenic conditions enables exploration of the relations between the adsorption geometry, electronic state, and vibrational fingerprints of individual molecules. TERS capability of reflecti ...

Amer Chemical Soc2024

High-order geometric integrators for the variational Gaussian wavepacket dynamics and application to vibronic spectra at finite temperature

Roya Moghaddasi Fereidani

Molecular quantum dynamics simulations are essential for understanding many fundamental phenomena in physics and chemistry. They often require solving the time-dependent Schrödinger equation for molecular nuclei, which is challenging even for medium-sized ...

EPFL2024

Iterative removal of sources to model the turbulent electromotive force

Salim Bennouna, Abhijit Bhausaheb Bendre

We describe a novel method to compute the components of dynamo tensors from direct magnetohydrodynamic (MHD) simulations. Our method relies upon an extension and generalization of the standard H & ouml;gbom CLEAN algorithm widely used in radio astronomy to ...

Oxford Univ Press2024

Stencil-Based Selective Surface Functionalization of Silicon Nanowires in 3D Device Architectures for Next-Generation Biochemical Sensors

Yusuf Leblebici

Surface functionalization of 1D materials such as silicon nanowires is a critical preparation technology for biochemical sensing. However, existing nonselective functionalization techniques result in nonlocal binding and contamination, with potential devic ...

Amer Chemical Soc2024