Scholars@Duke
Hilmar Lapp

Hilmar Lapp CV

Dir, IT
Biostatistics & Bioinformatics
Hilmar.Lapp@duke.edu
Box 90090, North Building 119, Durham, NC 27708
304 Research Drive, North Building 119, Durham, NC 27708
CV

Selected Publications

Hierarchical Conditioning of Diffusion Models Using Tree-of-Life for Studying Species Evolution

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 2025 A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image rep ... Full text Cite

A FAIR and modular image-based workflow for knowledge discovery in the emerging field of imageomics

Journal Article Methods in Ecology and Evolution · June 1, 2024 Image-based machine learning tools are an ascendant ‘big data’ research avenue. Citizen science platforms, like iNaturalist, and museum-led initiatives provide researchers with an abundance of data and knowledge to extract. These include extraction of meta ... Full text Cite

Meeting Report for the Phenoscape TraitFest 2023 with Comments on Organising Interdisciplinary Meetings

Journal Article Biodiversity Information Science and Standards · March 6, 2024 The Phenoscape project has developed ontology-based tools and a knowledge base that enables the integration and discovery of phenotypes across species from the scientific literature. The Phenoscape TraitFest 2023 event aimed to promote innovative a ... Full text Cite

rphenoscate: An R package for semantics-aware evolutionary analyses of anatomical traits

Journal Article Methods in Ecology and Evolution · October 1, 2023 Organismal anatomy is a hierarchical system of anatomical entities often imposing dependencies among multiple morphological characters. Ontologies provide a formal and computable framework for incorporating prior biological knowledge about anatomical depen ... Full text Cite

Discovering Novel Biological Traits from Images Using Phylogeny-Guided Neural Networks

Conference Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining · August 6, 2023 Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often ... Full text Cite

Assessing Bayesian Phylogenetic Information Content of Morphological Data Using Knowledge From Anatomy Ontologies.

Journal Article Systematic biology · October 2022 Morphology remains a primary source of phylogenetic information for many groups of organisms, and the only one for most fossil taxa. Organismal anatomy is not a collection of randomly assembled and independent "parts", but instead a set of dependent and hi ... Full text Open Access Cite

Phyloreferences: Tree-Native, Reproducible, and Machine-Interpretable Taxon Concepts

Journal Article Philosophy, Theory, and Practice in Biology · January 27, 2022 Evolutionary and organismal biology have become inundated with data. At the same rate, we are experiencing a surge in broader evolutionary and ecological syntheses for which tree-thinking is the staple for a variety of post-tree analyses. To fully ... Full text Cite

A new phylogenetic data standard for computable clade definitions: the Phyloreference Exchange Format (Phyx).

Journal Article PeerJ · January 2022 To be computationally reproducible and efficient, integration of disparate data depends on shared entities whose matching meaning (semantics) can be computationally assessed. For biodiversity data one of the most prevalent shared entities for linking data ... Full text Open Access Cite

JPhyloRef: a tool for testing and resolving phyloreferences

Journal Article Journal of Open Source Software · August 14, 2021 Full text Cite

Seed Patterns for Modeling Trees

Conference Studies in Health Technology and Informatics · May 7, 2021 Trees - i.e., the type of data structure known under this name - are central to many aspects of knowledge organization.We investigate some central design choices concerning the ontological modeling of such trees. In particular, we consider the limits of wh ... Full text Cite

Enabling Machines to Integrate Biodiversity Data with Evolutionary Knowledge

Journal Article Biodiversity Information Science and Standards · October 2, 2020 Most biological data and knowledge are directly or indirectly linked to biological taxa via taxon names. Using taxon names is one of the most fundamental and ubiquitous ways in which a wide range of biological data are integrated, aggregated, and i ... Full text Cite

A Logical Model of Homology for Comparative Biology.

Journal Article Systematic biology · March 2020 There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies ... Full text Open Access Cite

Application programming interfaces for knowledge transfer and generation in the life sciences and healthcare.

Journal Article NPJ Digit Med · 2020 Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. The electronic health record (EHR) ... Full text Open Access Link to item Cite

All the Clades in the World: Building a Semantically-Rich and Testable Ontology of Phylogenetic Clade Definitions

Journal Article Biodiversity Information Science and Standards · May 21, 2018 Taxonomic names are ambiguous as identifiers of biodiversity data, as they refer to a particular concept of a taxon in an expert’s mind (Kennedy et al. 2005). This ambiguity is particularly problematic when attempting to reconcile taxonomic names f ... Full text Cite

Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding.

Journal Article Cell Syst · April 25, 2018 Paralogous transcription factors (TFs) are oftentimes reported to have identical DNA-binding motifs, despite the fact that they perform distinct regulatory functions. Differential genomic targeting by paralogous TFs is generally assumed to be due to intera ... Full text Link to item Cite

Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology

Chapter · 2018 The study of how the observable features of organisms, i.e., their phenotypes, result from the complex interplay between genetics, development, and the environment, is central to much research in biology. The varied language used in the description of phen ... Full text Cite

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).

Journal Article F1000Research · January 2018 In 2018, the annual Bioinformatics Open Source Conference was held for the first time in conjunction with the Galaxy Community Conference, as an experiment to see if we could reach people in the bioinformatics community who aren't part of the audience attr ... Full text Open Access Cite

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.

Journal Article Database : the journal of biological databases and curation · January 2018 Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic in ... Full text Open Access Cite

Reasoning over anatomical homology in the Phenoscape KB

Conference CEUR Workshop Proceedings · January 1, 2018 The Phenoscape project (www.phenoscape.org) has semantically annotated the features of species from the comparative literature, enabling links between candidate genes and novel species phenotypes for which they might be responsible. To enable discovery of ... Cite

Community and Code: Nine Lessons from Nine NESCent Hackathons

Journal Article · June 6, 2017 In recent years, there has been an explosion in the popularity of hackathons — creative, participant-driven meetings at which software developers gather for an intensive bout of programming, often organized in teams. Hackathons have tangible and intangible ... Full text Cite

Developing educational resources for population genetics in R: an open and collaborative approach.

Journal Article Molecular ecology resources · January 2017 The r computing and statistical language community has developed a myriad of resources for conducting population genetic analyses. However, resources for learning how to carry out population genetic analyses in r are scattered and often incomplete, which c ... Full text Cite

apex: phylogenetics with multiple genes.

Journal Article Molecular ecology resources · January 2017 Genetic sequences of multiple genes are becoming increasingly common for a wide range of organisms including viruses, bacteria and eukaryotes. While such data may sometimes be treated as a single locus, in practice, a number of biological and statistical p ... Full text Open Access Cite

The 2017 Bioinformatics Open Source Conference (BOSC).

Journal Article F1000Research · January 2017 The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biolo ... Full text Open Access Cite

RNeXML: A package for reading and writing richly annotated phylogenetic, character and trait data in R

Journal Article Methods in Ecology and Evolution · March 1, 2016 NeXML is a powerful and extensible exchange standard recently proposed to better meet the expanding needs for phylogenetic data and metadata sharing. Here we present the RNeXML package, which provides users of the r programming language with easy-to-use to ... Full text Open Access Cite

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Journal Article PLoS computational biology · February 2016 The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological resea ... Full text Open Access Cite

Phenoscape: Identifying Candidate Genes for Evolutionary Phenotypes.

Journal Article Molecular biology and evolution · January 2016 Phenotypes resulting from mutations in genetic model organisms can help reveal candidate genes for evolutionarily important phenotypic changes in related taxa. Although testing candidate gene hypotheses experimentally in nonmodel organisms is typically dif ... Full text Open Access Cite

Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity. - Accepted at pacific symposium on biocomputing, 2016

Conference Pacific Symposium on Biocomputing · January 1, 2016 There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organis ... Cite

Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

Journal Article PloS one · January 2016 BackgroundIn recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic sear ... Full text Open Access Cite

The 2016 Bioinformatics Open Source Conference (BOSC).

Journal Article F1000Research · January 2016 Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software developm ... Full text Open Access Cite

Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies.

Journal Article Systematic biology · November 2015 The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer re ... Full text Open Access Cite

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.

Journal Article Genesis (New York, N.Y. : 2000) · August 2015 The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discove ... Full text Cite

Data Carpentry: Workshops to Increase Data Literacy for Researchers

Journal Article International Journal of Digital Curation · March 18, 2015 In many domains the rapid generation of large amounts of data is fundamentally changing how research is done. The deluge of data presents great opportunities, but also many challenges in managing, analyzing and sharing data. However, good training resource ... Full text Cite

Finding our way through phenotypes.

Journal Article PLoS biology · January 2015 Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing pheno ... Full text Open Access Cite

The Bioinformatics Open Source Conference (BOSC) 2013.

Journal Article Bioinformatics (Oxford, England) · January 2015 Full text Cite

Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy.

Journal Article Database : the journal of biological databases and curation · January 2015 The diverse phenotypes of living organisms have been described for centuries, and though they may be digitized, they are not readily available in a computable form. Using over 100 morphological studies, the Phenoscape project has demonstrated that by annot ... Full text Open Access Cite

Summary of the First Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE1)

Journal Article Journal of Open Research Software · July 9, 2014 Challenges related to development, deployment, and maintenance of reusable software for science are becoming a growing concern. Many scientists’ research increasingly depends on the quality and availability of software upon which their works are built. To ... Full text Open Access Cite

Presence-absence reasoning for evolutionary phenotypes

Conference Phenotype Day at International Conference on Intelligent Systems for Molecular Biology (ISBM 2014) · July 2014 Open Access Cite

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

Journal Article Journal of biomedical semantics · February 2014 The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual BioHackathons hosted in Japan for the past five years ... Full text Open Access Cite

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Journal Article Journal of biomedical semantics · January 2014 BackgroundPhenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address s ... Full text Open Access Cite

Liberating Our Beautiful Trees: A Call to Arms

Journal Article · 2014 Visual media can captivate, fascinate, and inspire. Whether skillfully taken photographs or artfully crafted visual illustrations, visuals convey beauty in ways that words can’t, and can tell even complex stories to audiences that might otherwise not liste ... Full text Cite

What is an anatomy ontology?

Journal Article Anatomical record (Hoboken, N.J. : 2007) · December 2013 Full text Cite

The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes.

Journal Article Journal of biomedical semantics · November 2013 BackgroundA hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data. Ideally, there would be a single, expansive, authoritative taxonomy that includes extinct and extant taxa, information on synonyms and ... Full text Open Access Cite

The Bioinformatics Open Source Conference (BOSC) 2013

Journal Article · October 20, 2013 The 14th annual Bioinformatics Open Source Conference (BOSC) was held in Berlin in July 2013, bringing together over 100 bioinformatics researchers, developers and users of open source software. Since its inception in 2000, BOSC has been organised as a Spe ... Full text Cite

Response to GBIF request for consultation on data licenses

Other · September 16, 2013 Response to GBIF request for consultation on data licenses ... Full text Cite

Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.

Journal Article BMC bioinformatics · May 2013 BackgroundScientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a l ... Full text Open Access Cite

The PLOS Computational Biology Software Section

Journal Article PLoS computational biology · November 2012 Cite

RCN4GSC Workshop Report: Managing Data at the Interface of Biodiversity and (Meta)Genomics, March 2011.

Journal Article Standards in genomic sciences · October 2012 Building on the planning efforts of the RCN4GSC project, a workshop was convened in San Diego to bring together experts from genomics and metagenomics, biodiversity, ecology, and bioinformatics with the charge to identify potential for positive interaction ... Full text Open Access Cite

NeXML: rich, extensible, and verifiable representation of comparative data and metadata.

Journal Article Systematic biology · July 2012 In scientific research, integration and synthesis require a common understanding of where data come from, how much they can be trusted, and what they may be used for. To make such an understanding computer-accessible requires standards for exchanging richl ... Full text Open Access Cite

500,000 fish phenotypes: The new informatics landscape for evolutionary and developmental biology of the vertebrate skeleton.

Journal Article Zeitschrift fur angewandte Ichthyologie = Journal of applied ichthyology · June 2012 The rich phenotypic diversity that characterizes the vertebrate skeleton results from evolutionary changes in regulation of genes that drive development. Although relatively little is known about the genes that underlie the skeletal variation among fish sp ... Full text Open Access Cite

PHENOSCAPE: A NEW ANATOMICAL ONTOLOGY OF VERTEBRATES

Conference JOURNAL OF VERTEBRATE PALEONTOLOGY · January 1, 2012 Link to item Cite

A unified anatomy ontology of the vertebrate skeletal system.

Journal Article PloS one · January 2012 The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning a ... Full text Open Access Cite

Integrating anatomy and phenotype ontologies with taxonomic hierarchies

Conference CEUR Workshop Proceedings · December 1, 2011 Cite

Overview of FEED, the feeding experiments end-user database.

Journal Article Integrative and comparative biology · August 2011 The Feeding Experiments End-user Database (FEED) is a research tool developed by the Mammalian Feeding Working Group at the National Evolutionary Synthesis Center that permits synthetic, evolutionary analyses of the physiology of mammalian feeding. The tas ... Full text Open Access Cite

Organizing our knowledge of biodiversity

Journal Article Bulletin of the American Society for Information Science and Technology · April 2011 Full text Cite

Similarity between semantic description sets: addressing needs beyond data integration

Conference Proceedings of the First International Workshop on Linked Science (LISC 2011) · 2011 Descriptive information is easy to understand and communicate in natural language. Examples in the biological realm include the cellular functions of proteins and the phenotypes exhibited by organisms. Large latent stores of such descriptive data are store ... Cite

Integrating anatomy and phenotype ontologies with taxonomic hierarchies

Conference ICBO: International Conference on Biomedical Ontology (2011) Proceedings · 2011 Cite

The Chado Natural Diversity module: a new generic database schema for large-scale phenotyping and genotyping data.

Journal Article Database : the journal of biological databases and curation · January 2011 Linking phenotypic with genotypic diversity has become a major requirement for basic and applied genome-centric biological research. To meet this need, a comprehensive database backend for efficiently storing, querying and analyzing large experimental data ... Full text Open Access Cite

Meeting Report: BioSharing at ISMB 2010.

Journal Article Standards in genomic sciences · December 2010 This report summarizes the proceedings of the one day BioSharing meeting held at the Intelligent Systems for Molecular Biology (ISMB) 2010 conference in Boston, MA, USA This inaugural BioSharing event was hosted by the Genomic Standards Consortium as part ... Full text Open Access Cite

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

Journal Article J. Biomed. Semantics · August 2010 ABSTRACT: Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire d ... Full text Open Access Cite

The teleost anatomy ontology: anatomical representation for the genomics age.

Journal Article Systematic biology · July 2010 The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to th ... Full text Open Access Cite

The Primate Life History Database: A unique shared ecological data resource.

Journal Article Methods in ecology and evolution · June 2010 The importance of data archiving, data sharing, and public access to data has received considerable attention. Awareness is growing among scientists that collaborative databases can facilitate these activities.We provide a detailed description of the colla ... Full text Cite

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

Journal Article PloS one · May 2010 BackgroundThe wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage t ... Full text Open Access Cite

Phenex: ontological annotation of phenotypic diversity.

Journal Article PloS one · May 2010 BackgroundPhenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed ... Full text Open Access Cite

Linking big: the continuing promise of evolutionary synthesis.

Journal Article Evolution; international journal of organic evolution · April 2010 Synthetic science promises an unparalleled ability to find new meaning in old data, extant results, or previously unconnected methods and concepts, but pursuing synthesis can be a difficult and risky endeavor. Our experience as biologists, informaticians, ... Full text Cite

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

Journal Article Evolutionary bioinformatics online · January 2007 In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collabora ... Cite

Open source tools and toolkits for bioinformatics: significance, and where are we?

Journal Article Briefings in bioinformatics · September 2006 This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Sour ... Full text Cite

Data and animal management software for large-scale phenotype screening.

Journal Article Mammalian genome : official journal of the International Mammalian Genome Society · April 2006 The mouse N-ethyl-N-nitrosourea (ENU) mutagenesis program at the Genomics Institute of the Novartis Research Foundation (GNF) uses MouseTRACS to analyze phenotype screens and manage animal husbandry. MouseTRACS is a Web-based laboratory informatics system ... Full text Cite

Large-scale profiling of Rab GTPase trafficking networks: the membrome.

Journal Article Molecular biology of the cell · August 2005 Rab GTPases and SNARE fusion proteins direct cargo trafficking through the exocytic and endocytic pathways of eukaryotic cells. We have used steady state mRNA expression profiling and computational hierarchical clustering methods to generate a global overv ... Full text Cite

Exploring trafficking GTPase function by mRNA expression profiling: use of the SymAtlas web-application and the Membrome datasets.

Journal Article Methods in enzymology · January 2005 Despite complete sequencing of the human and mouse genomes, functional annotation of novel gene function still remains a major challenge in mammalian biology. Emerging strategies to help elucidate unknown gene function include the analysis of tissue-specif ... Full text Cite

Applications of a rat multiple tissue gene expression data set.

Journal Article Genome research · April 2004 With the sequencing and assembly of the rat genome comes the difficult task of assigning functions to genes. Tissue localization of gene expression gives some information about the potential role of a gene in physiology. Various examples of the utility of ... Full text Cite

A gene atlas of the mouse and human protein-encoding transcriptomes.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · April 2004 The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom ar ... Full text Cite

Robust DNA microarray image analysis

Journal Article Machine Vision and Applications · October 1, 2003 DNA microarrays are an increasingly important tool that allow biologists to gain insight into the function of thousands of genes in a single experiment. Common to all array-based approaches is the necessity to analyze digital images of the scanned DNA arra ... Full text Cite

The Bioperl toolkit: Perl modules for the life sciences.

Journal Article Genome research · October 2002 The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life ... Full text Cite

Molecular classification of human carcinomas by use of gene expression signatures.

Journal Article Cancer research · October 2001 Classification of human tumors according to their primary anatomical site of origin is fundamental for the optimal treatment of patients with cancer. Here we describe the use of large-scale RNA profiling and supervised machine learning algorithms to constr ... Cite

A generic and robust approach for the analysis of spot array images

Journal Article Proceedings of SPIE-The International Society for Optical Engineering · January 1, 2001 We present a generic and robust image analysis approach applicable to image data resulting from a broad class of hybridization experiments. The ultimate image analysis goal is to automatically assign a quantity to every array element (spot), giving informa ... Full text Cite

Robust spot fitting for genetic spot array images

Conference IEEE International Conference on Image Processing · December 1, 2000 In this paper we address the problem of reliably fitting parametric and semi-parametric models to high density spot array images obtained in gene expression experiments. The goal is to measure the amount of genetic material at specific spot locations. Many ... Cite

Robust parametric and semi-parametric spot fitting for spot array images.

Journal Article Proceedings. International Conference on Intelligent Systems for Molecular Biology · January 2000 In this paper we address the problem of reliably fitting parametric and semi-parametric models to spots in high density spot array images obtained in gene expression experiments. The goal is to measure the amount of label bound to an array element. A lot o ... Cite

Robust Parametric and Semi-parametric Spot Fitting for Spot Array Images

Conference Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology, ISMB 2000 · January 1, 2000 In this paper we address the problem of reliably fitting parametric and semi-parametric models to spots in high density spot array images obtained in gene expression experiments. The goal is to measure the amount of label bound to an array element. A lot o ... Cite

Automatic grid fitting for genetic spot array images containing guide spots

Conference Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) · January 1, 1999 In the domain of biotechnology array-based methods are used to gain rapid access to genetic information based on the signals of the individual array elements (spots). For an automated analysis of the spots it is necessary to fit a grid to the spots in the ... Full text Cite

Software Engineering as Instrumentation for the Long Tail of Scientific Software

Other The vast majority of the long tail of scientific software, the myriads of tools that implement the many analysis and visualization methods for different scientific fields, is highly specialized, purpose-built for a research project, and has to rely on comm ... Full text Cite

On the Ontological Modeling of Trees

Conference Proceedings of the 8th Workshop on Ontology Design and Patterns (WOP 2017) Trees -- i.e., the type of data structure known under this name -- are central to many aspects of knowledge organization. We investigate some central design choices concerning the ontological modeling of such trees. In particular, we consider the limits of ... Open Access Link to item Cite

An Ontology-Based System for Querying Life in a Post-Taxonomic Age

Dataset Grant proposal (project description and references cited) to the US National Science Foundation, Advances in Biological Informatics (ABI) program as Collaborative Research. Funded in 2015. Files include public abstract as submitted to NSF. ... Full text Cite