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Deep image reconstruction from human brain activity

January 14, 2019

Deep image reconstruction from human brain activity

Image credit: Shen et al, pcbi.1006633.

Celebrating 1000 Simple Rules!

Our Ten Simple Rules series has published its 100th article. Check out the entire collection here!

Collection

01/14/2019

Research Article

PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data

Here, Hsu et al. present PAIRUP-MS, a suite of computational methods designed to analyze unknown, unidentified signals across multiple mass spectrometry-based profiling datasets. Specifically, PAIRUP-MS contains a flexible imputation-based approach for pairing up unknown signals across datasets, allowing for meta-analysis of matched signals across studies that would otherwise be incompatible.

Image credit: Hsu et al, pcbi.1006734.

PAIRUP-MS: Pathway analysis and imputation to relate unknowns in profiles from mass spectrometry-based metabolite data

Recently Published Articles

Current Issue

Current Issue December 2018

01/17/2019

Research Article

Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila

González, Jafari et al. present a model describing how the main regulatory cluster of the olfactory receptor Or59b drives transcription of this gene in Drosophila. The RNAp equilibrium probability is computed in terms of the occupancy probabilities of the single TFs of the cluster to the corresponding binding sites, and of the interaction rules among TFs and RNAp, using experimental data to tune the model parameters.


Image credit: González, Jafari et al, pcbi.1006709.

Thermodynamic model of gene regulation for the Or59b olfactory receptor in Drosophila

01/15/2019

Research Article

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

Binding small molecules to proteins often involves large conformational changes in the latter, which open pathways to the binding site. Pinpointing these rare events in large scale computations of specific protein-ligand complexes is expensive and to a great extent serendipitous. Dube et al. show that binding pathways can be discovered from short simulations of the apo-protein without waiting for a binding event.

Image credit: Dube et al, pcbi.1006665.

On identifying collective displacements in apo-proteins that reveal eventual binding pathways

01/17/2019

Research Article

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

To investigate the downstream signaling of a well-studied receptor tyrosine kinase, the insulin-like growth factor 1 receptor, Erickson et al. formulated and analyzed 45 cell line-specific mathematical models, which account for recruitment of 18 different binding partners to six sites of receptor autophosphorylation in IGF1R.

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

Image credit: Erickson et al, pcbi.1006706.

01/11/2019

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Complexity

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Complexity

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