Robin Haw
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View article: Advancing curation of viral life cycles, host interactions, and therapeutics in Reactome
Advancing curation of viral life cycles, host interactions, and therapeutics in Reactome Open
Reactome (reactome.org) is a manually curated, peer-reviewed, open-source, open-access pathway knowledgebase of essential human cellular functions. Reactome includes viral life cycles that capture a broad range of virus-induced human patho…
View article: Overture: an open-source genomics data platform
Overture: an open-source genomics data platform Open
Background Next-generation sequencing has created many new technological challenges in organizing and distributing genomics datasets, which now can routinely reach petabyte scales. Coupled with data-hungry artificial intelligence and machi…
View article: AI-augmented human biocuration in Reactome
AI-augmented human biocuration in Reactome Open
View article: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes Open
Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting…
View article: The Reactome Pathway Knowledgebase 2024
The Reactome Pathway Knowledgebase 2024 Open
The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated a…
View article: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes Open
Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome…
View article: Illuminate the Functions of Dark Proteins Using the Reactome‐IDG Web Portal
Illuminate the Functions of Dark Proteins Using the Reactome‐IDG Web Portal Open
Understudied or dark proteins have the potential to shed light on as‐yet undiscovered molecular mechanisms that underlie phenotypes and suggest innovative therapeutic approaches for many diseases. The Reactome‐IDG (Illuminating the Druggab…
View article: Functional Annotation of Disease Variants in Reactome
Functional Annotation of Disease Variants in Reactome Open
<p>Supplementary Tables and Supplementary Methods for the research article "Functional Annotation of Disease Variants in Reactome".</p>
View article: Illuminating Dark Proteins using Reactome Pathways
Illuminating Dark Proteins using Reactome Pathways Open
Limited knowledge about a substantial portion of protein coding genes, known as “dark” proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehe…
View article: Illuminating Dark Proteins using Reactome Pathways
Illuminating Dark Proteins using Reactome Pathways Open
Limited knowledge about a substantial portion of protein coding genes, known as "dark" proteins, hinders our understanding of their functions and potential therapeutic applications. To address this, we leveraged Reactome, the most comprehe…
View article: JBrowse 2: a modular genome browser with views of synteny and structural variation
JBrowse 2: a modular genome browser with views of synteny and structural variation Open
View article: Using the Reactome Database
Using the Reactome Database Open
Pathway databases provide descriptions of the roles of proteins, nucleic acids, lipids, carbohydrates, and other molecular entities within their biological cellular contexts. Pathway‐centric views of these roles may allow for the discovery…
View article: JBrowse Jupyter: a Python interface to JBrowse 2
JBrowse Jupyter: a Python interface to JBrowse 2 Open
Motivation JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically they have …
View article: Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways
Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways Open
Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we…
View article: Illuminating Dark Proteins using Reactome Pathways
Illuminating Dark Proteins using Reactome Pathways Open
Diseases are often the consequence of proteins or protein complexes that are non-functional or that function improperly. An active area of research has focused on the identification of molecules that can interact with defective proteins an…
View article: JBrowse 2: A modular genome browser with views of synteny and structural variation
JBrowse 2: A modular genome browser with views of synteny and structural variation Open
We present JBrowse 2, a general-purpose genome annotation browser offering enhanced visualization of complex structural variation and evolutionary relationships. JBrowse 2 retains the core features of the open-source JavaScript genome brow…
View article: JBrowse Jupyter: A Python interface to JBrowse 2
JBrowse Jupyter: A Python interface to JBrowse 2 Open
A bstract Motivation JBrowse Jupyter is a package that aims to close the gap between Python programming and genomic visualization. Web-based genome browsers are routinely used for publishing and inspecting genome annotations. Historically …
View article: Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase Open
Abstract Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturba…
View article: Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms
Erratum To: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms Open
View article: COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms
COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms Open
View article: The reactome pathway knowledgebase 2022
The reactome pathway knowledgebase 2022 Open
The Reactome Knowledgebase (https://reactome.org), an Elixir core resource, provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and ac…
View article: COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms Open
View article: R interface to the reactome graph database
R interface to the reactome graph database Open
View article: COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms Open
We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the dis…
View article: Expansion of reactome functional interaction network to allow exposure of knowledge space of understudied proteins in the context of biological pathways
Expansion of reactome functional interaction network to allow exposure of knowledge space of understudied proteins in the context of biological pathways Open
View article: The reactome pathway knowledgebase
The reactome pathway knowledgebase Open
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations in a single consist…
View article: Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 Open
The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and a…
View article: Reactome and ORCID—fine-grained credit attribution for community curation
Reactome and ORCID—fine-grained credit attribution for community curation Open
Reactome is a manually curated, open-source, open-data knowledge base of biomolecular pathways. Reactome has always provided clear credit attribution for authors, curators and reviewers through fine-grained annotation of all three roles at…
View article: The Reactome Pathway Knowledgebase
The Reactome Pathway Knowledgebase Open
The Reactome Knowledgebase (https://reactome.org) provides molecular details of signal transduction, transport, DNA replication, metabolism, and other cellular processes as an ordered network of molecular transformations-an extended versio…
View article: Reactome enhanced pathway visualization
Reactome enhanced pathway visualization Open
Motivation Reactome is a free, open-source, open-data, curated and peer-reviewed knowledge base of biomolecular pathways. Pathways are arranged in a hierarchical structure that largely corresponds to the GO biological process hierarchy, al…