Federico Comitani
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View article: Widespread hypertranscription in aggressive human cancers
Widespread hypertranscription in aggressive human cancers Open
Cancers are often defined by the dysregulation of specific transcriptional programs; however, the importance of global transcriptional changes is less understood. Hypertranscription is the genome-wide increase in RNA output. Hypertranscrip…
View article: Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling Open
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability…
View article: Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling
Extraction and high-throughput sequencing of oak heartwood DNA: assessing the feasibility of genome-wide DNA methylation profiling Open
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability…
View article: Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival
Lineage-defined leiomyosarcoma subtypes emerge years before diagnosis and determine patient survival Open
Leiomyosarcomas (LMS) are genetically heterogeneous tumors differentiating along smooth muscle lines. Currently, LMS treatment is not informed by molecular subtyping and is associated with highly variable survival. While disease site conti…
View article: Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling
Extraction and high-throughput sequencing of oak heartwood DNA: Assessing the feasibility of genome-wide DNA methylation profiling Open
Tree ring features are affected by environmental factors and therefore are the basis for dendrochronological studies to reconstruct past environmental conditions. Oak wood often provides the data for these studies because of the durability…
View article: Simulation data for 'Extraction and high-throughput sequencing of oak heartwood DNA - assessing the feasibility of genome-wide DNA methylation profiling'
Simulation data for 'Extraction and high-throughput sequencing of oak heartwood DNA - assessing the feasibility of genome-wide DNA methylation profiling' Open
Studies of the methylation state of DNA preserved in oak heartwood can help identify epigenetic tree ring features informing on past environmental conditions. Heartwood contains little DNA; large amounts of phenolic compounds are known to …
View article: Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution
Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution Open
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activ…
View article: fcomitani/SimpSOM: v1.3.4
fcomitani/SimpSOM: v1.3.4 Open
SimpSOM, a lightweight Python library for Kohonen Self-Organising Maps
View article: <i>Trans</i>–<i>Cis</i> Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment
<i>Trans</i>–<i>Cis</i> Proline Switches in a Pentameric Ligand-Gated Ion Channel: How They Are Affected by and How They Affect the Biomolecular Environment Open
Pentameric ligand-gated ion channels (pLGICs) are important neuroreceptors, embedded in neuronal membranes, that mediate fast synaptic transmission. The molecular details of their working mechanisms have still to be fully unravelled due to…
View article: A Multiscale Simulation Approach to Modeling Drug–Protein Binding Kinetics
A Multiscale Simulation Approach to Modeling Drug–Protein Binding Kinetics Open
Drug-target binding kinetics has recently emerged as a sometimes critical determinant of in vivo efficacy and toxicity. Its rational optimization to improve potency or reduce side effects of drugs is, however, extremely difficult. Molecula…
View article: Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells Open
In all living organisms, coenzyme A (CoA) is an essential cofactor with a unique design allowing it to function as an acyl group carrier and a carbonyl-activating group in diverse biochemical reactions. It is synthesized in a highly conser…
View article: Models and trajectories of GLUTAMINE SYNTHETASE with palmitoyl-coenzyme A
Models and trajectories of GLUTAMINE SYNTHETASE with palmitoyl-coenzyme A Open
These are the models and molecular dynamics trajectories obtained for the paper Role of glutamine synthetase in angiogenesis beyond glutamine synthesis [G. Eelen et al. Nature 2018 vol. 561 (7721) pp. 63-69].The PDB files (human.pdb and ba…
View article: Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution
Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution Open
The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relative…
View article: Data Files for Mapping the Conformational Free Energy of Aspartic Acid in the Gas Phase and in Aqueous Solution
Data Files for Mapping the Conformational Free Energy of Aspartic Acid in the Gas Phase and in Aqueous Solution Open
The data are divided in sub-projects where different systems were simulated with different force fields.CHARMM_: simulations run with the CHARMM36 force fieldAMBER_: simulations run with the AMBER FF99SB-ILDN force fieldOPLS_: simulations …
View article: The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations
The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations Open
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of a neurotransmitter, but the details of this process are st…
View article: The free energy landscape of GABA binding to a pentameric ligand-gated ion channel and its disruption by mutations
The free energy landscape of GABA binding to a pentameric ligand-gated ion channel and its disruption by mutations Open
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are important neuroreceptors that mediate fast synaptic transmission. They are activated by the binding of a neurotransmitter, but the details of this process are st…
View article: The free energy landscape of GABA binding to a pentameric ligand-gated\n ion channel and its disruption by mutations
The free energy landscape of GABA binding to a pentameric ligand-gated\n ion channel and its disruption by mutations Open
Pentameric ligand-gated ion channels (pLGICs) of the Cys-loop superfamily are\nimportant neuroreceptors that mediate fast synaptic transmission. They are\nactivated by the binding of a neurotransmitter, but the details of this process\nare…
View article: The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations – Data
The Free Energy Landscape of GABA Binding to a Pentameric Ligand-Gated Ion Channel and Its Disruption by Mutations – Data Open
List of data files:WT_Input_Output.tar.gzE204A_Input_Ouput.tar.gzR111A_Input_Ouptut.tar.gzWT Trajectories (.dcd)E204A Trajectories (.dcd)R111A Trajectories (.dcd)The data are divided in three projects. WT: files related to the wild-type RD…