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Benchmarked approaches for reconstruction of in vitro cell lineages and in silico models of C. elegans and M. musculus developmental trees

期刊: CELL SYSTEMS, 2021; 12 (8)

The recent advent of CRISPR and other molecular tools enabled the reconstruction of cell lineages based on induced DNA mutations and promises to solve......

TAMEP are brain tumor parenchymal cells controlling neoplastic angiogenesis and progression

期刊: CELL SYSTEMS, 2021; 12 (3)

Aggressive brain tumors like glioblastoma depend on support by their local environment and subsets of tumor parenchymal cells may promote specific pha......

Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies

期刊: CELL SYSTEMS, 2021; 12 (3)

The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. H......

MONN: A Multi-objective Neural Network for Predicting Compound-Protein Interactions and Affinities

期刊: CELL SYSTEMS, 2020; 10 (4)

Computational approaches for understanding compound-protein interactions (CPIs) can greatly facilitate drug development. Recently, a number of deep-le......

Encoding Membrane-Potential-Based Memory within a Microbial Community

期刊: CELL SYSTEMS, 2020; 10 (5)

Cellular membrane potential plays a key role in the formation and retrieval of memories in the metazoan brain, but it remains unclear whether such mem......

A High-Throughput Genome-Integrated Assay Reveals Spatial Dependencies Governing Tcf7l2 Binding

期刊: CELL SYSTEMS, 2020; 11 (3)

Predicting where transcription factors bind in the genome from their in vitro DNA-binding affinity is confounded by the large number of possible inter......

Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity

期刊: CELL SYSTEMS, 2020; 11 (6)

Determining genes that orchestrate cell differentiation in development and disease remains a fundamental goal of cell biology. This study establishes ......

SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles

期刊: CELL SYSTEMS, 2020; 11 (6)

Protein-protein interactions (PPIs) play critical functional and regulatory roles in cellular processes. They are essential for macromolecular complex......

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

期刊: CELL SYSTEMS, 2020; 10 (3)

Here, we present Scribe (https://github.com/aristoteleo/scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between gen......

iSeq 2.0: A Modular and Interchangeable Toolkit for Interaction Screening in Yeast

期刊: CELL SYSTEMS, 2019; 8 (4)

We developed a flexible toolkit for combinatorial screening in Saccharomyces cerevisiae, which generates large libraries of cells, each uniquely barco......

JIF:8.64

Compression Generated by a 3D Supracellular Actomyosin Cortex Promotes Embryonic Stem Cell Colony Growth and Expression of Nanog and Oct4

期刊: CELL SYSTEMS, 2019; 9 (2)

Mechanical factors play critical roles in mammalian development. Here, we report that colony-growing mouse embryonic stem cells (mESCs) generate signi......

JIF:8.64

Overdosage of Balanced Protein Complexes Reduces Proliferation Rate in Aneuploid Cells

期刊: CELL SYSTEMS, 2019; 9 (2)

Cells with complex aneuploidies display a wide range of phenotypic abnormalities. However, the molecular basis for this has been mainly studied in tri......

JIF:8.64

Network Topologies That Can Achieve Dual Function of Adaptation and Noise Attenuation

期刊: CELL SYSTEMS, 2019; 9 (3)

Many signaling systems execute adaptation under circumstances that require noise attenuation. Here, we identify an intrinsic trade-off existing betwee......

JIF:8.64

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