ArticleBMC bioinformatics2014
PSEUDOMARKER 2.0: efficient computation of likelihoods using NOMAD.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- Multiple association studies identify 3 novel candidate genes for teat number trait in Danish Landrace and Large White pigs: BRINP3, LIN52, and UBE3B.Journal of animal science · 2025Article
- Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy.Nature genetics · 2024Article
- PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data.Briefings in bioinformatics · 2021Review
- Novel Linkage Peaks Discovered for Diabetic Nephropathy in Individuals With Type 1 Diabetes.Diabetes · 2021Article
- Variants in regulatory elements of PDE4D associate with major mental illness in the Finnish population.Molecular psychiatry · 2021Article
- Neuregulin signaling pathway in smoking behavior.Translational psychiatry · 2017Article
- Article
- A genome-wide screen for acrophobia susceptibility loci in a Finnish isolate.Scientific reports · 2016Article
- Article
- AMIGO-Kv2.1 Potassium Channel Complex Is Associated With Schizophrenia-Related Phenotypes.Schizophrenia bulletin · 2016Article
- Linkage analyses in Caribbean Hispanic families identify novel loci associated with familial late-onset Alzheimer's disease.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2015Article
- Genetic variants associated with susceptibility to psychosis in late-onset Alzheimer's disease families.Neurobiology of aging · 2015Article
- Genetic linkage analysis in the age of whole-genome sequencing.Nature reviews. Genetics · 2015Review
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundPSEUDOMARKER is a software package that performs joint linkage and linkage disequilibrium analysis between a marker and a putative disease locus. A key feature of PSEUDOMARKER is that it can combine case-controls and pedigrees of varying structure into a single unified analysis. Thus it maximizes the full likelihood of the data over marker allele frequencies or conditional allele frequencies on disease and recombination fraction.
resultsThe new version 2.0 uses the software package NOMAD to maximize likelihoods, resulting in generally comparable or better optima with many fewer evaluations of the likelihood functions.
conclusionsAfter being modified substantially to use modern optimization methods, PSEUDOMARKER version 2.0 is more robust and substantially faster than version 1.0. NOMAD may be useful in other bioinformatics problems where complex likelihood functions are optimized.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.