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James A Yorke

Publications and source records attributed to James A Yorke.

9 recordsLinked to original sources
PubMed2025

Efficient evidence-based genome annotation with EviAnn.

For many years, machine learning-based ab initio gene finding approaches have been central components of eukaryotic genome annotation pipelines, and they remain so today. The reliance on these approaches was originally sustained by the high cost and low availability of gene expression data, a primary source of evidence for gene annotation along with protein homology. However, innovations in modern sequencing technologies have revolutionized the acquisition of gene expression data, allowing scientists to rely more heavily on this class of evidence. In addition, proteins found in a multitude of well-annotated genomes represent another invaluable resource for gene annotation. Existing annotation packages often underutilize these data sources, which prompted us to develop EviAnn (Evidence-based Annotator), a novel evidence-based eukaryotic gene annotation system. EviAnn takes a strongly data-driven approach, building the exon-intron structure of genes from transcript alignments or protein-sequence homology rather than from purely ab initio gene finding techniques. We show that when provided with the same input data, EviAnn consistently outperforms current state-of-the-art packages including BRAKER3, MAKER2, and FINDER, while utilizing considerably less computer time. Annotation of a mammalian genome can be completed in less than an hour on a single multi-core server. EviAnn is freely available under an open-source license from https://github.com/alekseyzimin/EviAnn_release and from Bioconda as "eviann".

Journal Article↗
PubMed2006

Reconciling different infectivity estimates for HIV-1.

In our article, "HIV-1 Epidemics Driven by Late Stage Disease," we conclude that the probability of transmission of HIV through promiscuous or casual sexual contacts is significantly higher in the third or symptomatic stage of the disease. Our results differ greatly from those of the current literature. The primary stage or first stage has been reported to be the most infectious based on an article by Jacquez et al. More recently, the Wawer et al study of monogamous heterosexual couples in Rakai, Uganda found that the transmission of HIV was most likely to occur in the first 5 months after infection. We describe how the findings of the Wawer et al study might be compatible with our results. We also respond to a response by Koopman and Simon, who seem to criticize their own paper severely and choose not to defend it against our remarks.

Africa↗
PubMed2006

Edge of chaos in a parallel shear flow.

We study the transition between laminar and turbulent states in a Galerkin representation of a parallel shear flow, where a stable laminar flow and a transient turbulent flow state coexist. The regions of initial conditions where the lifetimes show strong fluctuations and a sensitive dependence on initial conditions are separated from the ones with a smooth variation of lifetimes by an object in phase space which we call the "edge of chaos." We describe techniques to identify and follow the edge, and our results indicate that the edge is a surface. For low Reynolds numbers we find that the surface coincides with the stable manifold of a periodic orbit, whereas at higher Reynolds numbers it is the stable set of a higher-dimensional chaotic object.

Journal Article↗
PubMed2006

Making forecasts for chaotic physical processes.

Making a prediction for a chaotic physical process involves specifying the probability associated with each possible outcome. Ensembles of solutions are frequently used to estimate this probability distribution. However, for a typical chaotic physical system and model of that system, no solution of remains close to for all time. We propose an alternative. This Letter shows how to inflate or systematically perturb the ensemble of solutions of so that some ensemble member remains close to for orders of magnitude longer than unperturbed solutions of . This is true even when the perturbations are significantly smaller than the model error.

Journal Article↗
PubMed2005

Convex error growth patterns in a global weather model.

We investigate the error growth, that is, the growth in the distance E between two typical solutions of a weather model. Typically E grows until it reaches a saturation value E(s). We find two distinct broad log-linear regimes, one for E below 2% of E(s) and the other for E above. In each, log (E/E(s)) grows as if satisfying a linear differential equation. When plotting d log(E)/dt vs log(E), the graph is convex. We argue this behavior is quite different from other dynamics problems with saturation values, which yield concave graphs.

Journal Article↗
PubMed2005

HIV epidemics driven by late disease stage transmission.

How infectious a person is when infected with HIV depends on what stage of the disease the person is in. We use 3 stages, which we call primary, asymptomatic, and symptomatic. It is important to have a systematic method for computing all 3 infectivities so that the measurements are comparable. Using robust modeling, we provide high-resolution estimates of semen infectivity by HIV disease stage. We find that the infectivity of the symptomatic stage is far higher, hence more potent, than the values that prior studies have used when modeling HIV transmission dynamics. The stage infectivity rates for semen are 0.024, 0.002, and 0.299 for the primary, asymptomatic, and symptomatic stages, respectively. Implications of our infectivity estimates and modeling for understanding heterosexual epidemics such as that in sub-Saharan African are explored.

Africa South of the Sahara↗
PubMed2004

Reducing storage requirements for biological sequence comparison.

MOTIVATION: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seed-and-extend' approach, in which occurrences of short subsequences called 'seeds' are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process. RESULTS: We present a simple and elegant method in which only a small fraction of seeds, called 'minimizers', needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.

Algorithms↗
PubMed2004

A preprocessor for shotgun assembly of large genomes.

The whole-genome shotgun (WGS) assembly technique has been remarkably successful in efforts to determine the sequence of bases that make up a genome. WGS assembly begins with a large collection of short fragments that have been selected at random from a genome. The sequence of bases at each end of the fragment is determined, albeit imprecisely, resulting in a sequence of letters called a "read." Each letter in a read is assigned a quality value, which estimates the probability that a sequencing error occurred in determining that letter. Reads are typically cut off after about 500 letters, where sequencing errors become endemic. We report on a set of procedures that (1) corrects most of the sequencing errors, (2) changes quality values accordingly, and (3) produces a list of "overlaps," i.e., pairs of reads that plausibly come from overlapping parts of the genome. Our procedures, which we call collectively the "UMD Overlapper," can be run iteratively and as a preprocessor for other assemblers. We tested the UMD Overlapper on Celera's Drosophila reads. When we replaced Celera's overlap procedures in the front end of their assembler, it was able to produce a significantly improved genome.

Animals↗