Machine learning for bioinformatics and neuroimaging

A Serra, P Galdi, R Tagliaferri - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Machine Learning (ML) is a well‐known paradigm that refers to the ability of systems to learn
a specific task from the data and aims to develop computer algorithms that improve with …

Integrating molecular networks with genetic variant interpretation for precision medicine

E Capriotti, K Ozturk, H Carter - Wiley Interdisciplinary Reviews …, 2019 - Wiley Online Library
More reliable and cheaper sequencing technologies have revealed the vast mutational
landscapes characteristic of many phenotypes. The analysis of such genetic variants has led …

Comparison of algorithms for the detection of cancer drivers at subgene resolution

E Porta-Pardo, A Kamburov, D Tamborero, T Pons… - Nature …, 2017 - nature.com
Understanding genetic events that lead to cancer initiation and progression remains one of
the biggest challenges in cancer biology. Traditionally, most algorithms for cancer-driver …

Pan-cancer mutational and transcriptional analysis of the integrator complex

A Federico, M Rienzo, C Abbondanza, V Costa… - International journal of …, 2017 - mdpi.com
The integrator complex has been recently identified as a key regulator of RNA Polymerase II-
mediated transcription, with many functions including the processing of small nuclear RNAs …

Open structural data in precision medicine

R Nussinov, H Jang, G Nir, CJ Tsai… - Annual review of …, 2022 - annualreviews.org
Three-dimensional protein structural data at the molecular level are pivotal for successful
precision medicine. Such data are crucial not only for discovering drugs that act to block the …

DMCM: a data-adaptive mutation clustering method to identify cancer-related mutation clusters

X Lu, X Qian, X Li, Q Miao, S Peng - Bioinformatics, 2019 - academic.oup.com
Motivation Functional somatic mutations within coding amino acid sequences confer growth
advantage in pathogenic process. Most existing methods for identifying cancer-related …

JNK1/2 represses Lkb1-deficiency-induced lung squamous cell carcinoma progression

J Liu, T Wang, CJ Creighton, SP Wu, M Ray… - Nature …, 2019 - nature.com
Mechanisms of lung squamous cell carcinoma (LSCC) development are poorly understood.
Here, we report that JNK1/2 activities attenuate Lkb1-deficiency-driven LSCC initiation and …

Delineation of functionally essential protein regions for 242 neurodevelopmental genes

S Iqbal, T Brünger, E Pérez-Palma, M Macnee… - Brain, 2023 - academic.oup.com
Neurodevelopmental disorders (NDDs), including severe paediatric epilepsy, autism and
intellectual disabilities are heterogeneous conditions in which clinical genetic testing can …

[HTML][HTML] Computational methods for detecting cancer hotspots

E Martinez-Ledesma, D Flores, V Trevino - Computational and Structural …, 2020 - Elsevier
Cancer mutations that are recurrently observed among patients are known as hotspots.
Hotspots are highly relevant because they are, presumably, likely functional. Known …

Lrt-cluster: a new clustering algorithm based on likelihood ratio test to identify driving genes

C Quan, F Liu, L Qi, Y Tie - Interdisciplinary Sciences: Computational Life …, 2023 - Springer
Somatic mutations often occur at high relapse sites in protein sequences, which indicates
that the location clustering of somatic missense mutations can be used to identify driving …