AIMC Topic: Computational Biology

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Current Projection Methods-Induced Biases at Subgroup Detection for Machine-Learning Based Data-Analysis of Biomedical Data.

International journal of molecular sciences
Advances in flow cytometry enable the acquisition of large and high-dimensional data sets per patient. Novel computational techniques allow the visualization of structures in these data and, finally, the identification of relevant subgroups. Correct ...

A deep neural network approach to predicting clinical outcomes of neuroblastoma patients.

BMC medical genomics
BACKGROUND: The availability of high-throughput omics datasets from large patient cohorts has allowed the development of methods that aim at predicting patient clinical outcomes, such as survival and disease recurrence. Such methods are also importan...

StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis.

BMC genomics
BACKGROUND: Recently, a number of studies have been conducted to investigate how plants respond to stress at the cellular molecular level by measuring gene expression profiles over time. As a result, a set of time-series gene expression data for the ...

Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries.

BMC genomics
BACKGROUND: Knowledge Base Commons (KBCommons) v1.1 is a universal and all-inclusive web-based framework providing generic functionalities for storing, sharing, analyzing, exploring, integrating and visualizing multiple organisms' genomics and integr...

Representation learning of genomic sequence motifs with convolutional neural networks.

PLoS computational biology
Although convolutional neural networks (CNNs) have been applied to a variety of computational genomics problems, there remains a large gap in our understanding of how they build representations of regulatory genomic sequences. Here we perform systema...

Avoidance of non-localizable obstacles in echolocating bats: A robotic model.

PLoS computational biology
Most objects and vegetation making up the habitats of echolocating bats return a multitude of overlapping echoes. Recent evidence suggests that the limited temporal and spatial resolution of bio-sonar prevents bats from separately perceiving the obje...

Latest trends in structure based drug design with protein targets.

Advances in protein chemistry and structural biology
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to d...

Modeling aspects of the language of life through transfer-learning protein sequences.

BMC bioinformatics
BACKGROUND: Predicting protein function and structure from sequence is one important challenge for computational biology. For 26 years, most state-of-the-art approaches combined machine learning and evolutionary information. However, for some applica...

A Deep Learning Model for Cell Growth Inhibition IC50 Prediction and Its Application for Gastric Cancer Patients.

International journal of molecular sciences
Heterogeneity in intratumoral cancers leads to discrepancies in drug responsiveness, due to diverse genomics profiles. Thus, prediction of drug responsiveness is critical in precision medicine. So far, in drug responsiveness prediction, drugs' molecu...