Single nucleotide polymorphism (SNP) is the most frequent form of DNA variation. The set of SNP's present in a chromosome (called the haplotype) is of interest in a wide area of applications in molecular biology and biomedicine, including diagnostic and medical therapy. In this paper we propose a new heuristic method for the problem of haplotype reconstruction for (portions of) a pair of homologous human chromosomes from a single individual (SIH). The problem is well known in literature and exact algorithms have been proposed for the case when no (or few) gaps are allowed in the input fragments. These algorithms, though exact and of polynomial complexity, are slow in practice. When gaps are considered no exact method of polynomial complexity is known. The problem is also hard to approximate with guarantees. Therefore fast heuristics have been proposed. In this paper we describe SpeedHap, a new heuristic method that is able to tackle the case of many gapped fragments and retains its effectiveness even when the input fragments have high rate of reading errors (up to 20%) and low coverage (as low as 3). We test SpeedHap on real data from the HapMap Project.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1109/TCBB.2008.67 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Mixed-Dimensional Semiconductors-Based Ternary Circuits with Tunable Negative Transconductance Characteristics.
ACS Appl Mater Interfaces
January 2025
Institute of Advanced Materials and Systems, Sookmyung Women's University, Seoul 04310, Republic of Korea.
Multivalued logic (MVL) systems, in which data are processed with more than two logic values, are considered a viable solution for achieving superior processing efficiency with higher data density and less complicated system complexity without further scaling challenges. Such MVL systems have been conceptually realized by using negative transconductance (NTC) devices whose channels consist of van der Waals (vdW) heterojunctions of low-dimensional semiconductors; however, their circuit operations have not been quite ideal for driving multiple stages in real circuit applications due to reasons such as a reduced output swing and poorly defined logic states. Herein, we demonstrate ternary inverter circuits with near rail-to-rail swing and three distinct logic states by employing vdW p-n heterojunctions of single-walled carbon nanotubes (SWCNT) and MoS where the SWCNT layer completely covers the MoS layer.
View Article and Find Full Text PDFLupus disease activity state and Foxp3 gene polymorphism.
Egypt J Immunol
January 2025
Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt.
The autoimmune disease systemic lupus erythematosus (SLE) is presented with many clinical symptoms. The transcription factor fork head box protein 3 (Foxp3) is expressed on regulatory T (T-reg) cells and essential for its development and function. Functional single-nucleotide polymorphisms (SNPs) in the Foxp3-3279 (rs3761548 C/A) gene influence SLE pathogenesis.
View Article and Find Full Text PDFDetection of STAT4 in Multiple Sclerosis patients by polymerase chain reaction and flowcytometry.
Egypt J Immunol
January 2025
Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut 71515, Egypt.
Multiple sclerosis (MS) is a disease of the central nervous system, characterized by progressive demyelination and inflammation. MS is characterized by immune system attacks on the myelin sheath surrounding nerve fibers. Genome-wide association studies revealed a polymorphism in the signal transducer and activator of transcription 4 (STAT4) gene that increases risk for MS.
View Article and Find Full Text PDFQuantifying Plasmodium vivax radical cure efficacy: a modelling study integrating clinical trial data and transmission dynamics.
Lancet Infect Dis
January 2025
Institut Pasteur, Université Paris Cité, G5 Épidémiologie et Analyse des Maladies Infectieuses, Paris, France. Electronic address:
Background: Plasmodium vivax forms dormant liver stages (hypnozoites) that can reactivate weeks to months after primary infection. Radical cure requires a combination of antimalarial drugs to kill both the blood-stage and liver-stage parasites. Hypnozoiticidal efficacy of the liver-stage drugs primaquine and tafenoquine cannot be estimated directly because hypnozoites are undetectable.
View Article and Find Full Text PDFHEBE: A novel chimeric chronokine for ameliorating memory deficits in Alzheimer's disease.
Biomed Pharmacother
January 2025
Institut de Neurociències (INc), Universitat Autònoma Barcelona, Bellaterra 08193, Spain; Vall d'Hebron Institut de Recerca (VHIR), Barcelona 08035, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain. Electronic address:
Alzheimer's disease (AD) is a prevalent neurodegenerative disorder characterized by amyloid-β and Tau protein depositions, with treatments focusing on single proteins have shown limited success due to the complexity of pathways involved. This study explored the potential of chronokines -proteins that modulate aging-related processes- as an alternative therapeutic approach. Specifically, we focused on a novel pleiotropic chimeric protein named HEBE, combining s-KL, sTREM2 and TIMP2, guided by bioinformatic analyses to ensure the preservation of each protein's conformation, crucial for their functions.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!