Matthew Studham
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View article: Toll-like receptor 8 activation induces a neutrophil inflammatory phenotype: therapeutic implications for the utility of toll-like receptor 8 inhibition
Toll-like receptor 8 activation induces a neutrophil inflammatory phenotype: therapeutic implications for the utility of toll-like receptor 8 inhibition Open
Excessive activation of toll-like receptor 7 and 8 (TLR7/8) plays a role in the pathogenesis of autoimmune diseases and is associated with negative outcomes from viral infections. Neutrophil activation is highly inflammatory and mediates t…
View article: Identifying lupus Patient Subsets Through Immune Cell Deconvolution of Gene Expression Data in Two Atacicept Phase II Studies
Identifying lupus Patient Subsets Through Immune Cell Deconvolution of Gene Expression Data in Two Atacicept Phase II Studies Open
Objective To use cell‐based gene signatures to identify patients with systemic lupus erythematous (SLE) in the phase II/III APRIL–SLE and phase IIb ADDRESS II trials most likely to respond to atacicept. Methods A published immune cell deco…
View article: Disease trajectory of <scp>SLE</scp> clinical endpoints and covariates affecting disease severity and probability of response: Analysis of pooled <scp>patient‐level</scp> placebo (<scp>Standard‐of‐Care</scp>) data to enable <scp>model‐informed</scp> drug development
Disease trajectory of <span>SLE</span> clinical endpoints and covariates affecting disease severity and probability of response: Analysis of pooled <span>patient‐level</span> placebo (<span>Standard‐of‐Care</span>) data to enable <span>model‐informed</span> drug development Open
Systemic lupus erythematosus (SLE) is an autoimmune disease affecting multiple organ systems. Many investigational agents have failed or shown only modest effects when added to standard of care (SoC) therapy in placebo‐controlled trials, a…
View article: Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms Open
View article: Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms
Perturbation-based gene regulatory network inference to unravel oncogenic mechanisms Open
The gene regulatory network (GRN) of human cells encodes mechanisms to ensure proper functioning. However, if this GRN is dysregulated, the cell may enter into a disease state such as cancer. Understanding the GRN as a system can therefore…
View article: FRI0208 IDENTIFYING LUPUS PATIENT SUBSETS AND SPECIFIC PHARMACODYNAMIC CHANGES THROUGH IMMUNE CELL DECONVOLUTION OF GENE EXPRESSION DATA IN ATACICEPT-TREATED PATIENTS IN THE APRIL-SLE STUDY
FRI0208 IDENTIFYING LUPUS PATIENT SUBSETS AND SPECIFIC PHARMACODYNAMIC CHANGES THROUGH IMMUNE CELL DECONVOLUTION OF GENE EXPRESSION DATA IN ATACICEPT-TREATED PATIENTS IN THE APRIL-SLE STUDY Open
View article: Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson
Identification of pharmacodynamic biomarker hypotheses through literature analysis with IBM Watson Open
Taken together, these results suggest that Watson for Drug Discovery's automatic relationship network identifies the majority of upstream and downstream genes in biological pathway networks and can be used to help with the identification a…
View article: 211 Identifying lupus patient subsets and specific pharmacodynamic changes through immune cell deconvolution of gene expression data in atacicept-treated patients in the APRIL-SLE study
211 Identifying lupus patient subsets and specific pharmacodynamic changes through immune cell deconvolution of gene expression data in atacicept-treated patients in the APRIL-SLE study Open
Background The Phase II/III APRIL-SLE study evaluated the safety and efficacy of atacicept in systemic lupus erythematosus (SLE). The goal of this post-hoc analysis was to use cell-based gene signatures on the APRIL-SLE gene expression dat…
View article: Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization
Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization Open
Soybean aphids (Aphis glycines Matsumura) are specialized insects that feed on soybean (Glycine max) phloem sap. Transcriptome analyses have shown that resistant soybean plants mount a fast response that limits aphid feeding …
View article: A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family
A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family Open
View article: Validation of a hairy roots system to study soybean-soybean aphid interactions
Validation of a hairy roots system to study soybean-soybean aphid interactions Open
The soybean aphid (Aphis glycines) is one of the main insect pests of soybean (Glycine max) worldwide. Genomics approaches have provided important data on transcriptome changes, both in the insect and in the plant, in response to the plant…
View article: GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties
GeneSPIDER – gene regulatory network inference benchmarking with controlled network and data properties Open
A key question in network inference, that has not been properly answered, is what accuracy can be expected for a given biological dataset and inference method.
View article: GeneSPIDER - Generation and Simulation Package for Informative Data ExploRation
GeneSPIDER - Generation and Simulation Package for Informative Data ExploRation Open
A range of tools are available to model, simulate and analyze gene regulatory networks (GRNs). However, these tools provide limited ability to control network topology, system dynamics, design of experiments, data properties, or noise char…