Publications related to A Statistical Guide to the Design of Deep Mutational Scanning Experiments

Related publications (30)

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

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

Anthony C Davison and Igor Rodionov's contribution to the Discussion of 'Estimating means of bounded random variables by betting' by Waudby-Smith and Ramdas

Igor Rodionov, Anthony Christopher Davison

We derive confidence intervals (CIs) and confidence sequences (CSs) for the classical problem of estimating a bounded mean. Our approach generalizes and improves on the celebrated Chernoff method, yielding the best closed-form "empirical-Bernstein" CSs and ...

Oxford Univ Press2024

Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures

Pilar Natalia Rodilla Ramírez, Christof Holliger, Aline Sondra Adler, Jaspreet Singh Saini, Laetitia Janine Andrée Cardona, Ruizhe Pei

Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted ...

Amer Soc Microbiology2024

Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods

Jaspreet Singh Saini

Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral ...

Amer Soc Microbiology2024

Reproductive isolation arises during laboratory adaptation to a novel hot environment

Ana Marija Jaksic

Background: Reproductive isolation can result from adaptive processes (e.g., ecological speciation and mutation-order speciation) or stochastic processes such as "system drift" model. Ecological speciation predicts barriers to gene flow between populations ...

BMC2024

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

The role of LRRK2 in lung adenocarcinoma

Aspasia Gkasti

Lung cancer is the leading cause of cancer-related deaths worldwide and the most common lung cancer subtype is lung adenocarcinoma (LUAD). Frequently mutated genes involve activating mutations in KRAS and loss of function mutations in TP53. LUADs primarily ...

EPFL2024

Fair real-time control of energy storage systems in active distribution networks in the presence of uncertainties

Plouton Grammatikos

The thesis explores the issue of fairness in the real-time (RT) control of battery energy storage systems (BESSs) hosted in active distribution networks (ADNs) in the presence of uncertainties by proposing and experimentally validating appropriate control ...

EPFL2024

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Christina Ernst

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Nature Portfolio2024

A FEM modelling workflow to simulate THM effects in the rock around nuclear waste packages

Matthias Timothee Stanislas Wojnarowicz

High-level waste, stemming from nuclear electricity generation poses significant environmental and safety concerns. Currently, high-level wastes are stored in interim facilities needing constant monitoring and waiting for a definitive solution. Deep geolog ...

EPFL2024

Anisotropic Adaptive Finite Elements for a p-Laplacian Problem

Marco Picasso, Paride Passelli

The p-Laplacian problem -del & sdot; ((mu + |del u|(p-2))del u) = f is considered, where mu is a given positive number. An anisotropic a posteriori residual-based error estimator is presented. The error estimator is shown to be equivalent, up to higher ord ...

Walter De Gruyter Gmbh2024

Multimodal transcriptomic atlases of mouse spinal cord injury

Matthieu Pierre Gautier

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

EPFL2024

Spectral Estimators for High-Dimensional Matrix Inference

Farzad Pourkamali

A key challenge across many disciplines is to extract meaningful information from data which is often obscured by noise. These datasets are typically represented as large matrices. Given the current trend of ever-increasing data volumes, with datasets grow ...

EPFL2024

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

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

Construction of sequencing libraries from a ribonucleic acid (rna) using tailing and ligation of cdna (tlc)

Didier Trono, Christina Ernst

The present invention provides a method for preparing a sequencing library from a ribonucleic acid (RNA) sample. ...

2023

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Saurabh Tomar

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

EPFL2023

Maximum likelihood bolometry for ASDEX upgrade experiments

Olivier Claude Martin Février, Riccardo Rossi

Bolometry is an essential diagnostic for calculating the power balances and for the understanding of different physical aspects of tokamak experiments. The reconstruction method based on the Maximum Likelihood (ML) principle, developed initially for JET, h ...

Iop Publishing Ltd2023

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