Publications related to Automated high-content phenotyping from the first larval stage till the onset of adulthood of the nematode Caenorhabditis elegans

Quantifying the Unknown: Data-Driven Approaches and Applications in Energy Systems

In light of the challenges posed by climate change and the goals of the Paris Agreement, electricity generation is shifting to a more renewable and decentralized pattern, while the operation of systems like buildings is increasingly electrified. This calls ...

EPFL2024

Spatial Distributions of Diarrheal Cases in Relation to Housing Conditions in Informal Settlements: A Cross-Sectional Study in Abidjan, Côte d’Ivoire

Jérôme Chenal, Vitor Pessoa Colombo, Jürg Utzinger

In addition to individual practices and access to water, sanitation, and hygiene (WASH) facilities, housing conditions may also be associated with the risk of diarrhea. Our study embraced a broad approach to health determinants by looking at housing depriv ...

2023

Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

Hamed Khakzad

Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

PUBLIC LIBRARY SCIENCE2023

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

Pascal Fua, Sean Lewis Hill, Amos Sironi, Jiancheng Yang, Jian Zhou, Siqi Liu, Xiang Li, Jie Zhou

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in m ...

2023

Systematic benchmarking of single-cell ATAC-sequencing protocols

Bart Deplancke, Jörn Pezoldt, Camille Lucie Germaine Lambert

Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

NATURE PORTFOLIO2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

One Fuzz Doesn’t Fit All: Optimizing Directed Fuzzing via Target-tailored Program State Restriction

Mathias Josef Payer

Fuzzing is the de-facto default technique to discover software flaws, randomly testing programs to discover crashing test cases. Yet, a particular scenario may only care about specific code regions (for, e.g., bug reproduction, patch or regression testing) ...

ASSOC COMPUTING MACHINERY2022

Bubble-enhanced ultrasonic microfluidic chip for rapid DNA fragmentation

Thomas Lehnert, Martinus Gijs, Lin Sun

DNA fragmentation is an essential process in developing genetic sequencing strategies, genetic research, as well as for the diagnosis of diseases with a genetic signature like cancer. Efficient on-chip DNA fragmentation protocols would be beneficial to pro ...

ROYAL SOC CHEMISTRY2022

Feature-based no-reference video quality assessment using Extra Trees

Arash Amini, Hatef Otroshi Shahreza

With the emergence of social networks and improvements in the internet speed, the video data has become an ever-increasing portion of the global internet traffic. Besides the content, the quality of a video sequence is an important issue at the user end wh ...

WILEY2022

Technological and computational advances driving high-throughput oncology

Christoph Merten, Leonie Kolmar, Alexis Louis Autour, Blandine Anne Catherine Vergier, Xiaoli Ma

Engineering and computational advances have opened many new avenues in cancer research, particularly when being exploited in interdisciplinary approaches. For example, the combination of microfluidics, novel sequencing technologies, and computational analy ...

ELSEVIER SCIENCE LONDON2022

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

The enhancement of DNA fragmentation in a bench top ultrasonic water bath with needle-induced air bubbles: Simulation and experimental investigation

Thomas Lehnert, Martinus Gijs, Yang Liu, Lin Sun

Shearing DNA to a certain size is the first step in many medical and biological applications, especially in next-generation gene sequencing technology. In this article, we introduced a highly efficient ultrasonic DNA fragmentation method enhanced by needle ...

AIP Publishing2022

An Introduction to MPEG-G: The First Open ISO/IEC Standard for the Compression and Exchange of Genomic Sequencing Data

Marco Mattavelli

The development and progress of high-throughput sequencing technologies have transformed the sequencing of DNA from a scientific research challenge to practice. With the release of the latest generation of sequencing machines, the cost of sequencing a whol ...

IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC2021

Physics-Inspired Structural Representations for Molecules and Materials

Félix Benedito Clément Musil, Michele Ceriotti, Andrea Grisafi

The first step in the construction of a regression model or a data-driven analysis, aiming to predict or elucidate the relationship between the atomic-scale structure of matter and its properties, involves transforming the Cartesian coordinates of the atom ...

AMER CHEMICAL SOC2021

Multi-ion-sensing emulator and multivariate calibration optimization by machine learning models

Giovanni De Micheli, Sandro Carrara, Mandresy Ivan Ny Hanitra, Francesca Criscuolo

One paramount challenge in multi-ion-sensing arises from ion interference that degrades the accuracy of sensor calibration. Machine learning models are here proposed to optimize such multivariate calibration. However, the acquisition of big experimental da ...

2021

Counting People by Estimating People Flows

Pascal Fua, Mathieu Salzmann, Weizhe Liu

Modern methods for counting people in crowded scenes rely on deep networks to estimate people densities in individual images. As such, only very few take advantage of temporal consistency in video sequences, and those that do only impose weak smoothness co ...

2022

Estimating Nonplanar Flow from 2D Motion-blurred Widefield Microscopy Images via Deep Learning

Michael Stefan Daniel Liebling, Adrian Shajkofci

Optical flow is a method aimed at predicting the movement velocity of any pixel in the image and is used in medicine and biology to estimate flow of particles in organs or organelles. However, a precise optical flow measurement requires images taken at hig ...

IEEE2021

How Asynchronous Events Encode Video

Martin Vetterli, Adam James Scholefield, Karen Adam

As event-based sensing gains in popularity, theoretical understanding is needed to harness this technology’s potential. Instead of recording video by capturing frames, event-based cameras have sensors that emit events when their inputs change, thus encodin ...

IEEE2021

Intestinal organoid cocultures with microbes

Devanjali Dutta

This protocol comprises various methods to coculture organoids (particularly human small intestinal and colon organoids) with microbes, including microinjection into the lumen and periphery of 3D organoids and exposure of organoids to microbes in a 2D laye ...

NATURE PORTFOLIO2021

Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC

Tamar Kohn, Timothy R. Julian, Carola Bänziger, Xavier Fernandez Cassi, Federica Cariti, Alex Tunas Corzon

The continuing emergence of SARS-CoV-2 variants of concern and variants of interest emphasizes the need for early detection and epidemiological surveillance of novel variants. We used genomic sequencing of 122 wastewater samples from three locations in Swi ...

2022