Benchmark and integration of resources for the estimation of human transcription factor activities

L Garcia-Alonso, CH Holland, MM Ibrahim… - Genome …, 2019 - genome.cshlp.org
The prediction of transcription factor (TF) activities from the gene expression of their targets
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …

Connecting omics signatures and revealing biological mechanisms with iLINCS

M Pilarczyk, M Fazel-Najafabadi, M Kouril… - Nature …, 2022 - nature.com
There are only a few platforms that integrate multiple omics data types, bioinformatics tools,
and interfaces for integrative analyses and visualization that do not require programming …

Single-cell-resolved differentiation of human induced pluripotent stem cells into pancreatic duct-like organoids on a microwell chip

S Wiedenmann, M Breunig, J Merkle… - Nature biomedical …, 2021 - nature.com
Creating in vitro models of diseases of the pancreatic ductal compartment requires a
comprehensive understanding of the developmental trajectories of pancreas-specific cell …

KEA3: improved kinase enrichment analysis via data integration

MV Kuleshov, Z **e, ABK London, J Yang… - Nucleic acids …, 2021 - academic.oup.com
Phosphoproteomics and proteomics experiments capture a global snapshot of the cellular
signaling network, but these methods do not directly measure kinase state. Kinase …

Oncogenic circRNA C190 promotes non–small cell lung cancer via modulation of the EGFR/ERK pathway

AA Ishola, CS Chien, YP Yang, Y Chien, AA Yarmishyn… - Cancer Research, 2022 - AACR
Lung cancers are the leading cause of cancer-related mortality worldwide, and the majority
of lung cancers are non–small cell lung carcinoma (NSCLC). Overexpressed or activated …

Inferring protein expression changes from mRNA in Alzheimer's dementia using deep neural networks

S Tasaki, J Xu, DR Avey, L Johnson, VA Petyuk… - Nature …, 2022 - nature.com
Identifying the molecular systems and proteins that modify the progression of Alzheimer's
disease and related dementias (ADRD) is central to drug target selection. However …

Integrated multi-omics analysis of Alzheimer's disease shows molecular signatures associated with disease progression and potential therapeutic targets

P Kodam, R Sai Swaroop, SS Pradhan… - Scientific reports, 2023 - nature.com
Alzheimer's disease (AD) is a progressive neurodegenerative disease characterized by the
formation of amyloid plaques implicated in neuronal death. Genetics, age, and sex are the …

Computational analysis of phosphoproteomics data in multi‐omics cancer studies

G Mantini, TV Pham, SR Piersma, CR Jimenez - Proteomics, 2021 - Wiley Online Library
Multiple types of molecular data for the same set of clinical samples are increasingly
available and may be analyzed jointly in an integrative analysis to maximize comprehensive …

LYN kinase programs stromal fibroblasts to facilitate leukemic survival via regulation of c-JUN and THBS1

AF Vom Stein, R Rebollido-Rios, A Lukas… - Nature …, 2023 - nature.com
Microenvironmental bystander cells are essential for the progression of chronic lymphocytic
leukemia (CLL). We have discovered previously that LYN kinase promotes the formation of a …

[HTML][HTML] New insights into extracellular and intracellular redox status in COVID-19 patients

MJ Tavassolifar, HA Aghdaei, O Sadatpour, S Maleknia… - Redox Biology, 2023 - Elsevier
Background The imbalance of redox homeostasis induces hyper-inflammation in viral
infections. In this study, we explored the redox system signature in response to SARS-COV …