Publications associées à Assemblage (bio-informatique)

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

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

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

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

Clement Helsens

Single-cell sequencing (sc-seq) provides a species agnostic tool to study cellular processes. However, these technologies are expensive and require sufficient cell quantities and biological replicates to avoid artifactual results. An option to address thes ...

LIFE SCIENCE ALLIANCE LLC2023

Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter

Christof Holliger, Julien Maillard, Aline Sondra Adler, Marco Pagni, Simon Marius Jean Poirier

Complete genomes can be recovered from metagenomes by assembling and binning DNA sequences into metagenome assembled genomes (MAGs). Yet, the presence of microdiversity can hamper the assembly and binning processes, possibly yielding chimeric, highly fragm ...

WILEY2022

Towards mouse genetic-specific RNA-sequencing read mapping

Maxime Jan, Ioannis Xenarios

Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using ...

2022

Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells

Wouter Saelens

We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimul ...

Nature Research2021

Variants in USP48 encoding ubiquitin hydrolase are associated with autosomal dominant non-syndromic hereditary hearing loss

Nicolas Jean Philippe Guex

Non-Syndromic Hereditary Hearing Loss (NSHHL) is a genetically heterogeneous sensory disorder with about 120 genes already associated. Through exome sequencing (ES) and data aggregation, we identified a family with six affected individuals and one unrelate ...

Oxford University Press2021

The methylome of the model arbuscular mycorrhizal fungus, Rhizophagus irregularis, shares characteristics with early diverging fungi and Dikarya

Natalia Gasilova, Laure Menin

Early-diverging fungi (EDF) are distinct from Dikarya and other eukaryotes, exhibiting high N6-methyldeoxyadenine (6mA) contents, rather than 5-methylcytosine (5mC). As plants transitioned to land the EDF sub-phylum, arbuscular mycorrhizal fungi (AMF; Glom ...

NATURE PORTFOLIO2021

A Crowdsourced Gameplay for Whole-Genome Assembly via Short Reads

Kalpani Anuradha Welivita

Next-generation sequencing has revolutionized the field of genomics by producing accurate, rapid and cost-effective genome analysis with the use of high throughput sequencing technologies. This has intensified the need for accurate and performance efficien ...

2020

Comparison of chitin‐induced natural transformation in pandemic Vibrio cholerae O1 El Tor strains

Melanie Blokesch, Sandrine Stutzmann

The human pathogen Vibrio cholerae serves as a model organism for many important processes ranging from pathogenesis to natural transformation, which has been extensively studied in this bacterium. Previous work has deciphered important regulatory circuits ...

2020

Genome Sequence Alignment - Design Space Exploration for Optimal Performance and Energy Architectures

David Atienza Alonso, Marina Zapater Sancho, Yasir Mahmood Qureshi, José Manuel Herruzo Ruiz

Next generation workloads, such as genome sequencing, have an astounding impact in the healthcare sector. Sequence alignment, the first step in genome sequencing, has experienced recent breakthroughs, which resulted in next generation sequencing (NGS). As ...

2020

Alkynyl Triazenes as Fluoroalkyne Surrogates: Regioselective Access to 4-Fluoro-2-pyridones by a Rh(III)-Catalyzed C–H Activation–Lossen Rearrangement–Wallach Reaction

Kay Severin, Nicolai Cramer, Carl Thomas Bormann, Jin Fay Tan

Fluorinated pyridones are an important scaffold displaying relevant biological activities. Efficient assembly strategies of pyridones are transition metal-catalyzed C–H annulations with alkynes. The inaccessibility and extreme lability of fluoro alkynes re ...

2020

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

Jacques Fellay, Chenjie Wan

The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 reservoir size and its long-term decay by analyzin ...

Nature Research2020

2D MoS2 nanopores: ionic current blockade height for clustering DNA events

Aleksandra Radenovic, Ke Liu

2D nanopores can be used to electrophoretically drive DNA molecules, which can in turn be identified through measurable electronic current blockades. In this work, we use experimental data from molybdenum disulfide nanopores threading DNA nucleotides and p ...

2019

Detection of dicistroviruses RNA in blood of febrile Tanzanian children

Mary-Anne Hartley, Thomas Junier

Fever is the leading cause of paediatric outpatient consultations in Sub-Saharan Africa. Although most are suspected to be of viral origin, a putative causative pathogen is not identified in over a quarter of these febrile episodes. Using a de novo assembl ...

2019

IMPACT: Interval-based Multi-pass Proteomic Alignment with Constant Traceback

James Richard Larus, Sahand Kashani, Stuart Anthony Byma

Darwin is a genomics co-processor that achieved a 15000x acceleration on long read assembly through innovative hardware and algorithm co-design. Darwins algorithms and hardware implementation were specifically designed for DNA analysis pipelines. This pape ...

2019

Long-Read-Based Genome Sequences of Pandemic and Environmental Vibrio cholerae Strains

Noémie Matthey, Melanie Blokesch, Natalia Carolina Drebes Dorr

The bacterium Vibrio cholerae exhibits two distinct lifestyles, one as an aquatic bacterium and the other as the etiological agent of the pandemic human disease cholera. Here, we report closed genome sequences of two seventh pandemic V. cholerae O1 El Tor ...

2018

Integrative approach to analyze the proximal region of the Trichonympha agilis centriole

Veronika Nemcíková Villímová

The centrosome, the major microtubule organizing center in animal cells, is composed of two orthogonally arranged centrioles and surrounding pericentriolar material. Centrioles are evolutionary conserved organelles characterized by a nine-fold symmetry of ...

EPFL2018

In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction

Bruno Lemaitre, Fanny Schüpfer, Florent François Masson, Mario Gonzalo Garcia Arraez

Endosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbio ...

2018

Scanning tunneling microscopy on large bio-molecular systems on surfaces

Sebastian Koslowski

The ever growing demand for the development of new technologies and materials has led to extensive studies inspired by biological functional complexes. Peptides with their outstanding ability to efficiently self-assemble can express a broad spectrum of int ...

EPFL2017