Qian Cheng
@qchengx1e3.bsky.social
470 followers
48 following
42 posts
Senior Editor at Nature Communications (Computational Biology, AI for Biotechnology). Science communications. PhD (Cantab). Views my own.
https://www.nature.com/subjects/computational-biology-and-bioinformatics/ncomms
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Qian Cheng
@qchengx1e3.bsky.social
· Aug 22
Multi-scale and multi-context interpretable mapping of cell states across heterogeneous spatial samples - Nature Communications
The alignment of heterogeneous spatial samples has become a growing challenge. Here, authors present a multi-scale, multi-context, and interpretable mapping strategy to map cells across space, time, a...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Aug 14
Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics - Nature Communications
Cells rely on limited numbers of transmembrane receptors to process signals from dynamic microenvironments. Using microfluidics and endogenous reporters, the authors track single cells to reveal how t...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Jul 22
Single cell and spatial alternative splicing analysis with Nanopore long read sequencing - Nature Communications
Single-cell isoform quantification using Nanopore long reads remains limited by sequencing errors. Here, authors present Longcell, a computational framework that corrects these errors and uncovers spl...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Jul 13
Quantification of transcript isoforms at the single-cell level using SCALPEL - Nature Communications
Single-cell RNA-seq facilitates the study of transcriptome diversity in individual cells. Here, authors introduce a tool for isoform quantification at the single-cell level using 3’ scRNA-seq data, co...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 13
Highly adaptable deep-learning platform for automated detection and analysis of vesicle exocytosis - Nature Communications
Activity recognition in live-cell imaging is laborious. Here, authors present, IVEA, a fully automated AI ImageJ plugin, that efficiently detects and classifies exocytosis events, from synaptic transm...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
ToxACoL: an endpoint-aware and task-focused compound representation learning paradigm for acute toxicity assessment - Nature Communications
Multi-species acute systemic toxicity assessment is fundamental for chemical classification, labelling and risk management. Here, the authors propose a machine learning paradigm, Adjoint Correlation L...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values - Nature Communications
Individual data types in a single cell multi-omic assay are often processed and clustered independently before combined for further analysis. Here, authors showed that binarized gene expression d...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
GPerturb: Gaussian process modelling of single-cell perturbation data - Nature Communications
Single-cell CRISPR screens enable high-throughput analysis of how genetic changes affect individual cells. Here, authors present GPerturb, a method that accurately detects and quantifies gene-level ef...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Modeling heterogeneous signaling dynamics of macrophages reveals principles of information transmission in stimulus responses - Nature Communications
To develop virtual cells, mathematical models must account for the heterogeneity of single cells. Here, authors develop virtual single cell NFκB signalling networks that recapitulate heterogenous expe...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Automated cell annotation and classification on histopathology for spatial biomarker discovery - Nature Communications
Histopathology is essential for diagnosing cancer, but cell annotation remains unreliable and inefficient. Here, authors develop a method using deep learning and immune-fluorescence-guided cell labell...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Cell Marker Accordion: interpretable single-cell and spatial omics annotation in health and disease - Nature Communications
Accurate cell type annotation is a major challenge in single-cell and spatial omics. Here, authors present a user-friendly platform providing robust automatic annotation and enhanced biological interp...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Accelerating cell culture media development using Bayesian optimization-based iterative experimental design - Nature Communications
Optimising operational conditions for biological systems is a complex task. Here, authors present a Bayesian optimisation-based iterative experimental design framework that integrates data generation,...
doi.org
Qian Cheng
@qchengx1e3.bsky.social
· Jul 7
Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy - Nature Communications
The cell nucleus coordinates diverse functions. Here, the authors utilise multiplexed super-resolution imaging to study how nuclear proteins are distributed relative to each other from the micro to th...
doi.org
Reposted by Qian Cheng
Rachel Won
@rachelpcwon.bsky.social
· Jun 13
Associate or Senior Editor, Nature Reviews Electrical Engineering
Job title: Associate or Senior Editor, Nature Reviews Electrical Engineering Location: Shanghai or New York – hybrid working model Closing date: 1st July 2025 About Springer Nature Group Springer Natu...
springernature.wd3.myworkdayjobs.com
Qian Cheng
@qchengx1e3.bsky.social
· Jun 6
A versatile information retrieval framework for evaluating profile strength and similarity - Nature Communications
Profiling assays measure thousands of features to uncover biological insights but lack reliable methods for quality evaluation. Here, the authors develop a versatile information retrieval framework to...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Jun 6
An AI-assisted fluorescence microscopic system for screening mitophagy inducers by simultaneous analysis of mitophagic intermediates - Nature Communications
Mitophagy is crucial for mitochondrial function and is implicated in Alzheimer’s disease. Here, the authors introduce an AI-assisted fluorescence microscopy system to track mitophagic intermediates in...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· May 28
CellFM: a large-scale foundation model pre-trained on transcriptomics of 100 million human cells - Nature Communications
Single-cell sequencing reveals cellular heterogeneity but is challenged by technical noise and batch effects. Here, authors present CellFM, an 800-million-parameter foundation model trained on 100 mil...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· May 8
Learning tissue representation by identification of persistent local patterns in spatial omics data - Nature Communications
Spatial omics reveal tissue structures and can aid patient stratification. The authors present a method to identify patterns in tissue patches, enabling analysis of disease progression and treatment r...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Apr 24
EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals - Nature Communications
Despite having structures for most proteins, we still do not know their function. Here, authors introduce EvoWeaver, a de novo method to identify genes working together using evolutionary information....
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Apr 21
scPRINT: pre-training on 50 million cells allows robust gene network predictions - Nature Communications
Authors present a state-of-the-art cell foundation model trained on 50 million cells. They show that the model generates a meaningful gene network and has zero-shot ability in various tasks.
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Apr 15
MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search - Nature Communications
Proteomics often misses co-fragmented peptides in DDA data. Here, the authors introduce MSFragger-DDA+, a database search tool that enhances peptide identification by searching the full isolation wind...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Apr 2
Statistical analysis of spatial patterns in tumor microenvironment images - Nature Communications
Immunotherapy is transforming cancer treatment, with immune cell distribution in the tumour microenvironment key to predicting outcomes. Here, authors provide a robust framework to analyse spatial pat...
www.nature.com
Qian Cheng
@qchengx1e3.bsky.social
· Mar 12
Computation-aided designs enable developing auxotrophic metabolic sensors for wide-range glyoxylate and glycolate detection - Nature Communications
Auxotrophic metabolic sensors (AMS) are vital for bioengineering but are often time-consuming to develop. Here, the authors present a workflow for designing versatile AMS, demonstrating their use for ...
www.nature.com