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List of works by Lawrence Hunter

8. Towards Property Rights in Personal Data

A FAULT MODEL FOR ONTOLOGY MAPPING, ALIGNMENT, AND LINKING SYSTEMS

A Goal-Based Approach to Intelligent Information Retrieval

A Little Bit of Chemistry

A TWENTIETH ANNIVERSARY TRIBUTE TO PSB

A UIMA wrapper for the NCBO annotator

scientific article

A bioinformatics tool to select sequences for microarray studies of mouse models of oncogenesis

scientific article published on 01 May 2002

A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools

scientific article

A critical review of PASBio's argument structures for biomedical verbs

scientific article published on 24 November 2006

A fault model for ontology mapping, alignment, and linking systems.

scientific article published on January 2007

A simulated MS/MS library for spectrum-to-spectrum searching in large scale identification of proteins

scientific article

A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation

scientific article published on August 2010

A survey of computational tools for downstream analysis of proteomic and other omic datasets

scientific article

A twentieth anniversary tribute to PSB.

scientific article published in January 2015

AMIA Board white paper: definition of biomedical informatics and specification of core competencies for graduate education in the discipline

scientific article published on 8 June 2012

ASSESSING AND COMBINING RELIABILITY OF PROTEIN INTERACTION SOURCES

Aging promotes acquisition of naive-like CD8+ memory T cell traits and enhanced functionalities

scientific article published on 12 September 2016

An introduction to effective use of enrichment analysis software

scientific article

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

scientific article

Anatomy, Physiology, and Systems Biology

Applying knowledge-driven mechanistic inference to toxicogenomics

scientific article published on 06 May 2020

Approximate subgraph matching-based literature mining for biomedical events and relations

scientific article

Assessing and combining reliability of protein interaction sources.

scientific article published on January 2007

BioCreAtIvE task1A: entity identification with a stochastic tagger

scientific article published on 24 May 2005

Biocomputing 2010

Biocomputing 2011

Biolink Model: A Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science ⬇️

scientific article

Biological Macromolecules

scholarly article published 16 January 2009

Biomedical discovery acceleration, with applications to craniofacial development

scientific article published in March 2009

Biomedical language processing: what's beyond PubMed?

scientific article

Building the next generation of quantitative biologists

scientific article published on January 2014

COMPUTATIONAL CHALLENGES OF MASS PHENOTYPING

Celebrating parasites

scientific article published on March 2017

Changes to NIH Grant System May Backfire

scientific article

Chapter 16: text mining for translational bioinformatics

scientific article

Circular clustering of protein dihedral angles by Minimum Message Length

scientific article published on 01 January 1996

Combining heterogenous data for prediction of disease related and pharmacogenes

scientific article (publication date: 2014)

Computational challenges of mass phenotyping ⬇️

scientific article published on January 1, 2013

Computationally efficient cluster representation in molecular sequence megaclassification.

scientific article published in January 1993

Concept annotation in the CRAFT corpus

scientific article

Concept recognition for extracting protein interaction relations from biomedical text

scientific article published on September 2008

Consistent visualizations of changing knowledge.

scientific article published on March 2009

Contrast and variability in gene names

article

Coreference annotation and resolution in the Colorado Richly Annotated Full Text (CRAFT) corpus of biomedical journal articles

scientific article

Corpus design for biomedical natural language processing

scholarly article published 2005

Corpus refactoring: a feasibility study

scientific article

Cross-species cluster co-conservation: a new method for generating protein interaction networks

scientific article

Current methodologies for translational bioinformatics

scientific article

Desiderata for ontologies to be used in semantic annotation of biomedical documents

scientific article

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

scientific article

Differential gene expression in human cerebrovascular malformations

scientific article published on February 2003

Disease and Its Treatment

EDGAR: extraction of drugs, genes and relations from the biomedical literature

scientific article published in January 2000

EXTRACTION OF GENOTYPE-PHENOTYPE-DRUG RELATIONSHIPS FROM TEXT:

Early detection of graft failure using the blood metabolic profile of a liver recipient

scientific article published in February 2007

Efficient Classification of Massive, Unsegmented Datastreams

Empirical data on corpus design and usage in biomedical natural language processing.

scientific article

Enrichment of OBO ontologies

scientific article published on 26 July 2006

Estimating Human Cognitive Capacities: A Response to Landauer*

article

Eukaryotes

Evaluation of genetic enhancement: will human wisdom properly acknowledge the value of evolution?

scientific article published on January 2005

Evaluation of lexical methods for detecting relationships between concepts from multiple ontologies.

scientific article

Evolution

Exact calculations of average power for the Benjamini-Hochberg procedure

scientific article published in January 2008

Examining linguistic shifts between preprints and publications

scientific article published on 01 February 2022

Expected Power for the False Discovery Rate with Independence

scientific article published on January 2008

Exploring species-based strategies for gene normalization.

scientific article

Extracting molecular binding relationships from biomedical text

article

Extraction of genotype-phenotype-drug relationships from text: from entity recognition to bioinformatics application

scientific article published on January 2010

FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

article

Finding GeneRIFs via gene ontology annotations.

scientific article

Finding relevant biomolecular features.

scientific article published on January 1993

Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution

scientific article published in July 2003

GEST: a gene expression search tool based on a novel Bayesian similarity metric

scientific article published in January 2001

Gating effects along mitral cell lateral dendrites.

scientific article published on 6 July 2007

Gene Ontology synonym generation rules lead to increased performance in biomedical concept recognition

scientific article

Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed

scientific article

Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma

scientific article

GeneRIF quality assurance as summary revision

scientific article

Getting started in text mining

scientific article

Go molecular function terms are predictive of subcellular localization

scientific article published on January 2005

Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

article

HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.

scientific article

High-precision biological event extraction with a concept recognizer

scientific article published in 2009

How interactive visualization can assist investigative analysis: Views and perspectives from domain experts

scholarly article published 2009

IMPLICATIONS OF COMPOSITIONALITY IN THE GENE ONTOLOGY FOR ITS CURATION AND USAGE

article

Identification of OBO nonalignments and its implications for OBO enrichment

scientific article published on 07 May 2008

Identification of divergent functions in homologous proteins by induction over conserved modules.

scientific article

Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats

scientific article

Identifying and classifying goals for scientific knowledge

scientific article published on 28 July 2021

Identifying chimerism in proteins using hidden Markov models of codon usage.

scientific article published on January 1997

Implications of compositionality in the gene ontology for its curation and usage

scientific article published on January 2005

Improving precision in concept normalization

scientific article published in January 2018

Improving protein function prediction methods with integrated literature data

scientific article

Innate differences in protein expression in the nucleus accumbens and hippocampus of inbred alcohol-preferring and -nonpreferring rats

scientific article published on July 2003

Integrated Term Weighting, Visualization, and User Interface Development for Bioinformation Retrieval

article

Interpersonal prosodic correlation in frontotemporal dementia

scientific article published on 17 June 2019

Intraglomerular gap junctions enhance interglomerular synchrony in a sparsely connected olfactory bulb network

scientific article published on 22 June 2017

Intrinsic evaluation of text mining tools may not predict performance on realistic tasks.

scientific article published on January 2008

Introducing meta-services for biomedical information extraction

scientific article published on September 2008

Introduction

Investigation of factors affecting prediction of protein-protein interaction networks by phylogenetic profiling

scientific article

KaBOB: ontology-based semantic integration of biomedical databases

scientific article

Kidney proteome changes provide evidence for a dynamic metabolism and regional redistribution of plasma proteins during torpor-arousal cycles of hibernation

scientific article

Knowledge Acquisition Planning: Results and Prospects

article

Knowledge-Driven Approaches to Genome-Scale Analysis

Knowledge-based biomedical Data Science

scholarly article by Lawrence Hunter published 17 October 2017 in Data Science

Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters

scientific article (publication date: 26 February 2014)

Leveraging Gene Ontology Annotations to Improve a Memory-Based Language Understanding System

article

Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology

scientific article

Manual curation is not sufficient for annotation of genomic databases

scientific article

MetaMap is a superior baseline to a standard document retrieval engine for the task of finding patient cohorts in clinical free text

scientific article published on 01 January 2011

Metabolic cycles in a circannual hibernator

scientific article

Mining Discriminative Distance Context of Transcription Factor Binding Sites on ChIP Enriched Regions

Mining Protein-Protein Interactions from GeneRIFs with OpenDMAP

article

Mining molecular binding terminology from biomedical text

scientific article

Molecular Bioethics

scholarly article published 16 January 2009

Molecular Biotechnology

scholarly article

Molecular profiling reveals prognostically significant subtypes of canine lymphoma

scientific article

Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance

scientific article published on 9 March 2008

Molecular subtypes of osteosarcoma identified by reducing tumor heterogeneity through an interspecies comparative approach

scientific article

Multicellular Organisms and Development

article

Multicompartment leaky integrate and fire neuron modeling with multiexponentials

Multistate proteomics analysis reveals novel strategies used by a hibernator to precondition the heart and conserve ATP for winter heterothermy

scientific article published on 13 September 2011

MutationFinder: a high-performance system for extracting point mutation mentions from text

scientific article

NO-BOUNDARY THINKING IN BIOINFORMATICS.

scientific article

Natural Language Processing and Systems Biology

Natural Language Processing and Systems Biology

Negotiating a Text Mining License for Faculty Researchers

New JBI emphasis on translational bioinformatics

Nominalization and alternations in biomedical language

scientific article

OWL-NETS: Transforming OWL Representations for Improved Network Inference.

scientific article published in January 2018

Ontologies for programs, not people

scientific article

Ontologies in biological data visualization

scientific article

Ontology quality assurance through analysis of term transformations

scientific article published on June 2009

Ontology translation: A case study on translating the Gene Ontology from English to German

article

OpenDMAP: an open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression

scientific article

Overview of BioCreative II gene mention recognition

scientific article published on September 2008

P-Hacking Lexical Richness Through Definitions of "Type" and "Token"

scientific article published on 01 August 2019

Parenthetically speaking: classifying the contents of parentheses for text mining.

scientific article

Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association

scientific article published on January 2015

Predicting enzyme function from sequence: a systematic appraisal

scientific article published on January 1997

Predicting protein linkages in bacteria: which method is best depends on task

scientific article

Primer session: Sense-making in molecular biology

scholarly article by Lawrence Hunter published in October 2011

Profiling impaired hepatic endoplasmic reticulum glycosylation as a consequence of ethanol ingestion

scientific article

Progress in computational molecular biology

article

Protein carbonylation in a murine model for early alcoholic liver disease

scientific article

Proteomic exploration of pancreatic islets in mice null for the alpha2A adrenergic receptor

scientific article published in August 2005

Proteomic informatics

scientific article published in January 2004

Rapid pattern development for concept recognition systems: application to point mutations

scientific article published in December 2007

Refactoring corpora

Refactoring corpora

Regional differences in subcutaneous adipose tissue gene expression

scientific article

Reporting actionable research results: shared secrets can save lives

scientific article

Reports of the AAAI 2014 Conference Workshops

Representing annotation compositionality and provenance for the Semantic Web.

scientific article

Reproducibility in Natural Language Processing: A Case Study of Two R Libraries for Mining PubMed/MEDLINE

article published in 2016

Rocky Mountain Conference on Bioinformatics Celebrates 10 Years ⬇️

scientific article published on May 30, 2013

Semantic Relations in Compound Nouns: Perspectives from Inter-Annotator Agreement

scientific article published in January 2017

Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery

article

Semantic role labeling for protein transport predicates

scientific article

Serial gene expression profiling in the intact human heart

scientific article published on 11 April 2006

Skeletal muscle proteomics: carbohydrate metabolism oscillates with seasonal and torpor-arousal physiology of hibernation

scientific article published on 24 August 2011

Software testing and the naturally occurring data assumption in natural language processing

article

Some memory, but no mind

Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences

scientific article

Synergizing genomic analysis with biological knowledge to identify and validate novel genes in pancreatic development

scientific article

Systems biology of facial development: contributions of ectoderm and mesenchyme

scientific article published on 28 March 2017

Teaching Research Ethics Better: Focus on Excellent Science, Not Bad Scientists ⬇️

scientific article published on April 18, 2013

The International Society for Computational Biology 10th Anniversary

scientific article

The Marriage of Phenomics and Genetical Genomics: A Systems Approach to Complex Trait Analysis

The PhenoGen informatics website: tools for analyses of complex traits

scientific article

The Processes of Life

The Qualitative Reasoning Neuron: a New Approach to Modeling in Computational Neuroscience

The Structure and Function of Bacteria

The compositional structure of Gene Ontology terms.

scientific article published on January 2004

The learning of function and the function of learning

The structural and content aspects of abstracts versus bodies of full text journal articles are different

scientific article

The textual characteristics of traditional and Open Access scientific journals are similar

scientific article

The topology of the bacterial co-conserved protein network and its implications for predicting protein function

scientific article

The use of explicit goals for knowledge to guide inference and learning

The use or generation of biomedical data and existing medicines to discover and establish new treatments for patients with rare diseases - recommendations of the IRDiRC Data Mining and Repurposing Task Force

scientific article published on 15 October 2019

Three Dimensions of Reproducibility in Natural Language Processing

Training the next generation of quantitative biologists in the era of big data

Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development

scientific article published on January 2003

Transcending inductive category formation in learning

article published in 1986

Translational Morphosyntax: Distribution of Negation in Clinical Records and Biomedical Journal Articles

scientific article published in January 2017

U-Compare bio-event meta-service: compatible BioNLP event extraction services

scientific article (publication date: 18 December 2011)

U-Compare: share and compare text mining tools with UIMA

scientific article

Using the Gene Ontology to Annotate Biomedical Journal Articles

Using the Gene Ontology to Annotate Biomedical Journal Articles

article

Visual analysis of biological data-knowledge networks

scientific article

Visual management of large scale data mining projects.

scientific article published in January 2000

Visualization and Language Processing for Supporting Analysis across the Biomedical Literature

scholarly article by Carsten Görg et al published 2010 in Lecture Notes in Computer Science

Visualization based on the Enzyme Commission nomenclature ⬇️

scientific article published on January 1, 1998

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