Controlling false discoveries in genome scans for selection

O François, H Martins, K Caye… - Molecular ecology, 2016 - Wiley Online Library
Population differentiation (PD) and ecological association (EA) tests have recently emerged
as prominent statistical methods to investigate signatures of local adaptation using …

AI-based structure prediction empowers integrative structural analysis of human nuclear pores

S Mosalaganti, A Obarska-Kosinska, M Siggel… - Science, 2022 - science.org
INTRODUCTION The eukaryotic nucleus protects the genome and is enclosed by the two
membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear …

Nuclear pores dilate and constrict in cellulo

CE Zimmerli, M Allegretti, V Rantos, SK Goetz… - Science, 2021 - science.org
INTRODUCTION The nucleus harbors and protects the genetic information in eukaryotes. It
is surrounded by the nuclear envelope, which separates the nucleoplasm from the cytosol …

Integrative structural modeling of macromolecular complexes using Assembline

V Rantos, K Karius, J Kosinski - Nature Protocols, 2022 - nature.com
Integrative modeling enables structure determination of macromolecular complexes by
combining data from multiple experimental sources such as X-ray crystallography, electron …

Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer: the NABUCCO trial

N van Dijk, A Gil-Jimenez, K Silina, K Hendricksen… - Nature medicine, 2020 - nature.com
Preoperative immunotherapy with anti-PD1 plus anti-CTLA4 antibodies has shown
remarkable pathological responses in melanoma and colorectal cancer. In NABUCCO …

A proteome-wide atlas of drug mechanism of action

DC Mitchell, M Kuljanin, J Li, JG Van Vranken… - Nature …, 2023 - nature.com
Defining the cellular response to pharmacological agents is critical for understanding the
mechanism of action of small molecule perturbagens. Here, we developed a 96-well-plate …

NetCoMi: network construction and comparison for microbiome data in R

S Peschel, CL Müller, E Von Mutius… - Briefings in …, 2021 - academic.oup.com
Motivation Estimating microbial association networks from high-throughput sequencing data
is a common exploratory data analysis approach aiming at understanding the complex …

Human gut microbiota from autism spectrum disorder promote behavioral symptoms in mice

G Sharon, NJ Cruz, DW Kang, MJ Gandal, B Wang… - Cell, 2019 - cell.com
Autism spectrum disorder (ASD) manifests as alterations in complex human behaviors
including social communication and stereotypies. In addition to genetic risks, the gut …

Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression

Y Ghavi-Helm, A Jankowski, S Meiers, RR Viales… - Nature …, 2019 - nature.com
Chromatin topology is intricately linked to gene expression, yet its functional requirement
remains unclear. Here, we comprehensively assessed the interplay between genome …

Network analysis and subsequent culturing reveal keystone taxa involved in microbial litter decomposition dynamics

H Zheng, T Yang, Y Bao, P He, K Yang, X Mei… - Soil Biology and …, 2021 - Elsevier
Plant litter decomposition in the soil is governed by microorganisms such as bacteria and
fungi that colonize lignocellulose residues during the decomposition process, and thus, the …