Publications
-
Fragment-based screening for enzyme inhibitors using calorimetry
This article describes how nanocalorimetry and conventional microcalorimetry can be used to screen compound libraries for enzyme inhibitors.
-
Diagnosis cloud: Sharing knowledge across cellular networks
This paper presents a novel diagnosis cloud framework that enables the extraction and transfer of knowledge from one network to another. It also presents use cases and requirements. We present…
-
The Time Is Right to Focus on Model Organism Metabolomes
We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to…
-
Representation and inference of cellular architecture for metabolic reconstruction and modeling
We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.
-
Can we replace curation with information extraction software?
Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are…
-
Crowd-sourcing and author submission as alternatives to professional curation
This perspective considers the significant experience accumulated by the bioinformatics community with these two alternatives to professional curation in the last 20 years...
-
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research.
-
Examining Change in K-3 Teachers’ Mathematical Knowledge, Attitudes, and Beliefs: The Case of Primarily Math
This study examines the impact of the Primarily Math Elementary Mathematics Specialist program on K-3 teachers’ mathematical content knowledge for teaching, attitudes toward learning mathematics, and beliefs about mathematics teaching…
-
Assessing Problem-Solving Process At Scale
This paper describes a hybrid approach to assessing process at scale in the context of the use of computational thinking practices during programming.
-
An Annotated Corpus and Method for Analysis of Ad-Hoc Structures Embedded in Text
We describe a method for identifying and performing functional analysis of structured regions that are embedded in natural language documents, such as tables or key-value lists.
-
Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.
-
Pathway Schools Initiative Developmental Evaluation-Learning Brief 1 (January 2016)
To support its Pathway Schools Initiative, The McKnight Foundation has engaged initiative leaders in a developmental evaluation (DE) led by SRI International and Child Trends.