A survey on computational models for predicting protein–protein interactions
Proteins interact with each other to play critical roles in many biological processes in cells.
Although promising, laboratory experiments usually suffer from the disadvantages of being …
Although promising, laboratory experiments usually suffer from the disadvantages of being …
Predicting protein–protein interactions from the molecular to the proteome level
Identification of protein–protein interactions (PPIs) is at the center of molecular biology
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
considering the unquestionable role of proteins in cells. Combinatorial interactions result in …
The UCSC genome browser database: 2018 update
Abstract The UCSC Genome Browser (https://genome. ucsc. edu) provides a web interface
for exploring annotated genome assemblies. The assemblies and annotation tracks are …
for exploring annotated genome assemblies. The assemblies and annotation tracks are …
HIPPIE v2. 0: enhancing meaningfulness and reliability of protein–protein interaction networks
G Alanis-Lobato, MA Andrade-Navarro… - Nucleic acids …, 2016 - academic.oup.com
The increasing number of experimentally detected interactions between proteins makes it
difficult for researchers to extract the interactions relevant for specific biological processes or …
difficult for researchers to extract the interactions relevant for specific biological processes or …
Factors influencing success of clinical genome sequencing across a broad spectrum of disorders
To assess factors influencing the success of whole-genome sequencing for mainstream
clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families …
clinical diagnosis, we sequenced 217 individuals from 156 independent cases or families …
KEA3: improved kinase enrichment analysis via data integration
Phosphoproteomics and proteomics experiments capture a global snapshot of the cellular
signaling network, but these methods do not directly measure kinase state. Kinase …
signaling network, but these methods do not directly measure kinase state. Kinase …
[HTML][HTML] The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
The human oral microbiome is the most studied human microflora, but 53% of the species
have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are …
have not yet been validly named and 35% remain uncultivated. The uncultivated taxa are …
[HTML][HTML] Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines
Highlights•Understanding the existing drug repositioning methods with a top-down
flowchart.•Prioritizing repositioning methods using their integrated knowledge and …
flowchart.•Prioritizing repositioning methods using their integrated knowledge and …
Towards a proteome-scale map of the human protein–protein interaction network
JF Rual, K Venkatesan, T Hao, T Hirozane-Kishikawa… - Nature, 2005 - nature.com
Systematic mapping of protein–protein interactions, or 'interactome'mapping, was initiated in
model organisms, starting with defined biological processes, and then expanding to the …
model organisms, starting with defined biological processes, and then expanding to the …
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM
Motivation: High-throughput data is providing a comprehensive view of the molecular
changes in cancer tissues. New technologies allow for the simultaneous genome-wide …
changes in cancer tissues. New technologies allow for the simultaneous genome-wide …