Predicting gene and protein expression levels from DNA and protein sequences with Perceiver

Identifying the oncogenic potential of gene fusions exploiting miRNAs

(2022) Marta Lovino et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations

(2022) Alessio Mascolini et al.   BMC BIOINFORMATICS

Predicting gene expression levels from DNA sequences and post-transcriptional information with transformers

(2022) Vittorio Pipoli et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Proteogenomic and metabolomic characterization of human glioblastoma

(2021) Liang-Bo Wang et al.   CANCER CELL

CEGSO: Boosting Essential Proteins Prediction by Integrating Protein Complex, Gene Expression, Gene Ontology, Subcellular Localization and Orthology Information

(2021) Wei Zhang et al.   Interdisciplinary Sciences-Computational Life Sciences

A proteogenomic portrait of lung squamous cell carcinoma

(2021) Shankha Satpathy et al.   CELL

Effective gene expression prediction from sequence by integrating long-range interactions

(2021) Žiga Avsec et al.   NATURE METHODS

An Integrated Systems Biology and Network-Based Approaches to Identify Novel Biomarkers in Breast Cancer Cell Lines Using Gene Expression Data

(2020) Abbas Khan et al.   Interdisciplinary Sciences-Computational Life Sciences

Data‐Independent Acquisition Mass Spectrometry‐Based Proteomics and Software Tools: A Glimpse in 2020

(2020) Fangfei Zhang et al.   PROTEOMICS

Predicting mRNA Abundance Directly from Genomic Sequence Using Deep Convolutional Neural Networks

(2020) Vikram Agarwal et al.   Cell Reports

Using Deep Learning to Extrapolate Protein Expression Measurements

(2020) Mitra Parissa Barzine et al.   PROTEOMICS

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk

(2018) Jian Zhou et al.   NATURE GENETICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging

(2016) Armando Fernandes et al.   PLoS One

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE