Warren Kibbe

Northwestern University, Preventive Medicine, Adjunct

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Sa1099 Collection of Patient Centered Outcomes in Esophageal Disease: An Open Source Web Based Framework

Gastroenterology, 2013

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease

The American Journal of Human Genetics, 2015

The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential ... more The Human Phenotype Ontology (HPO) is widely used in the rare disease community for differential diagnostics, phenotype-driven analysis of next-generation sequence-variation data, and translational research, but a comparable resource has not been available for common disease. Here, we have developed a concept-recognition procedure that analyzes the frequencies of HPO disease annotations as identified in over five million PubMed abstracts by employing an iterative procedure to optimize precision and recall of the identified terms. We derived disease models for 3,145 common human diseases comprising a total of 132,006 HPO annotations. The HPO now comprises over 250,000 phenotypic annotations for over 10,000 rare and common diseases and can be used for examining the phenotypic overlap among common diseases that share risk alleles, as well as between Mendelian diseases and common diseases linked by genomic location. The annotations, as well as the HPO itself, are freely available.

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Large-scale GO analysis reveals gene expression level and variation are functional and location related

The CAMDA 2007 META-analysis data set encompass many different tissue types in normal and disease... more The CAMDA 2007 META-analysis data set encompass many different tissue types in normal and disease states, which prompted us to ask a fundamental biological question: What are the essential genes in a living cell? Why the expression levels of some genes fluctuate a lot while the others are under tight control? Are there any relations between gene functions or locations with the gene expression levels and variation? We present a systems biology overview of life processes based on this analysis. We also model low-variance housekeeping genes (LoV-HKGs), which have practical use as internal control genes for RT-PCR experiments.

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Some Aspects of Analysis of Gene Array Data

Cancer Treatment and Research, 2002

Package ‘MassSpecWavelet’

The Informatics and Bioinformatics Infrastructure of a Nutrigenomics Biobank

Discovering the Path to Personalized Nutrition, 2006

... The coming wave of nutrigenomics and pharmacogenomics research that will utilize the next gen... more

Best practices for building interoperable systems for translational research

Nature Precedings, 2010

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Improved prediction of treatment response using microarrays and existing biological knowledge

Pharmacogenomics, 2006

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dictyBase: a new Dictyostelium discoideum genome database

Nucleic Acids Research, 2004

Dictyostelium discoideum is a powerful and genetically tractable model system used for the study ... more

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dictyBase, the model organism database for Dictyostelium discoideum

Nucleic Acids Research, 2006

dictyBase (http://dictybase.org) is the model organ-10 ism database (MOD) for the social amoeba D... more dictyBase (http://dictybase.org) is the model organ-10 ism database (MOD) for the social amoeba Dictyostelium discoideum. The unique biology and phylogenetic position of Dictyostelium offer a great opportunity to gain knowledge of processes not characterized in other organisms. The recent completion 15 of the 34 MB genome sequence, together with the sizable scientific literature using Dictyostelium as a research organism, provided the necessary tools to create a well-annotated genome. dictyBase has leveraged software developed by the Saccharomyces 20 Genome Database and the Generic Model Organism Database project. This has reduced the time required to develop a full-featured MOD and greatly facilitated our ability to focus on annotation and providing new functionality. We hope that manual curation of the 25 Dictyostelium genome will facilitate the annotation of other genomes.

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OligoCalc: an online oligonucleotide properties calculator

Nucleic Acids Research, 2007

We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA a... more We developed OligoCalc as a web-accessible, client-based computational engine for reporting DNA and RNA single-stranded and doublestranded properties, including molecular weight, solution concentration, melting temperature, estimated absorbance coefficients, inter-molecular self-complementarity estimation and intramolecular hairpin loop formation. OligoCalc has a familiar 'calculator' look and feel, making it readily understandable and usable. OligoCalc incorporates three common methods for calculating oligonucleotide-melting temperatures, including a nearest-neighbor thermodynamic model for melting temperature. Since it first came online in 1997, there have been more than 900 000 accesses of OligoCalc from nearly 200 000 distinct hosts, excluding search engines. OligoCalc is available at http://basic.north western.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well.

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Other riffs on cooperation are already showing how well a wiki could work

by Warren Kibbe, Simon Lin, and John Osborne

Nature, 2007

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Irrational Exuberance in Clinical Proteomics

Clinical Cancer Research, 2005

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Mining the Gene Wiki for functional genomic knowledge

BMC Genomics, 2011

Background: Ontology-based gene annotations are important tools for organizing and analyzing geno... more Background: Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology. Results: Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses. Conclusions: The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.

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nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays

by Warren Kibbe, Simon Lin, and Pan Du

Biology Direct, 2007

Background: Oligonucleotide probes that are sequence identical may have different identifiers bet... more Background: Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe.

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Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching

by Warren Kibbe, Simon Lin, and Pan Du

Bioinformatics, 2006

Motivation: A major problem for current peak detection algorithms is that noise in Mass Spectrome... more Motivation: A major problem for current peak detection algorithms is that noise in Mass Spectrometry (MS) spectra gives rise to a high rate of false positives. The false positive rate is especially problematic in detecting peaks with low amplitudes. Usually, various baseline correction algorithms and smoothing methods are applied before attempting peak detection. This approach is very sensitive to the amount of smoothing and aggressiveness of the baseline correction, which contribute to making peak detection results inconsistent between runs, instrumentation and analysis methods. Results: Most peak detection algorithms simply identify peaks based on amplitude, ignoring the additional information present in the shape of the peaks in a spectrum. In our experience, 'true' peaks have characteristic shapes, and providing a shape-matching function that provides a 'goodness of fit' coefficient should provide a more robust peak identification method. Based on these observations, a Continuous Wavelet Transform (CWT)-based peak detection algorithm has been devised that identifies peaks with different scales and amplitudes. By transforming the spectrum into wavelet space, the pattern-matching problem is simplified and additionally provides a powerful technique for identifying and separating the signal from the spike noise and colored noise. This transformation, with the additional information provided by the 2-D CWT coefficients can greatly enhance the effective Signal-to-Noise Ratio (SNR). Furthermore, with this technique no baseline removal or peak smoothing preprocessing steps are required before peak detection, and this improves the robustness of peak detection under a variety of conditions. The algorithm was evaluated with SELDI-TOF spectra with known polypeptide positions. Comparisons with two other popular algorithms were performed. The results show the CWT-based algorithm can identify both strong and weak peaks while keeping false positive rate low.

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A Detailed Analysis of Transcriptional Regulators Affecting the Saccharomyces Cerevisiae Heat-shock Gene Ssa1

A Collaborative Life Cycle Process for the Bioinformatics Core Facility

nuID: A Novel Identifier for Oligos, Ideal for Oligonucleotide-based Microarrays

Oligonucleotides (often simply referred to as oligos or oligomers), which are typically between 2... more Oligonucleotides (often simply referred to as oligos or oligomers), which are typically between 25 to 75 bases long, have been extensively used by DNA microarray manufacturers to detect the expression of different genes. An oligonucleotide sequence that is located on a specific bead or position on a microarray is usually referred to as the probe sequence, or just as the probe. Current microarrays by Affymetrix, Agilent, Illumina and others have tens of thousands or even hundreds of thousands of unique sequence probes in an array. The identification of the genes that hybridize to probe is a critical step in interpreting the results of microarrays.

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Heuristic-based Baseline Removal Algorithm for SELDI Proteomics Data

Motivation: Baseline removal, as the first preprocessing step of SELDI data, critically influence... more Motivation: Baseline removal, as the first preprocessing step of SELDI data, critically influences subsequent analysis steps. Current baseline removal algorithms of SELDI data, which are based on mathematical morphology, result in biased signal estimates. Due to the parameterization of current algorithms for baseline removal, noise and spectral signal distributions bias the removal results, which may lead to seemingly interesting but ultimately irreproducible results in downstream analysis.

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