Related Experiment Video

Updated: Jan 26, 2026

Designing CAD/CAM Surgical Guides for Maxillary Reconstruction Using an In-house Approach

Designing CAD/CAM Surgical Guides for Maxillary Reconstruction Using an In-house Approach

Published on: August 24, 2018

BHap: a novel approach for bacterial haplotype reconstruction

Xin Li¹, Samaneh Saadat¹, Haiyan Hu¹

¹Department of Computer Science, College of Medicine, University of Central Florida, Orlando, FL 32816, USA.

Bioinformatics (Oxford, England)

|April 21, 2019

Abstract

Motivation:

The bacterial haplotype reconstruction is critical for selecting proper treatments for diseases caused by unknown haplotypes. Existing methods and tools do not work well on this task, because they are usually developed for viral instead of bacterial populations.

Results:

In this study, we developed BHap, a novel algorithm based on fuzzy flow networks, for reconstructing bacterial haplotypes from next generation sequencing data. Tested on simulated and experimental datasets, we showed that BHap was capable of reconstructing haplotypes of bacterial populations with an average F1 score of 0.87, an average precision of 0.87 and an average recall of 0.88. We also demonstrated that BHap had a low susceptibility to sequencing errors, was capable of reconstructing haplotypes with low coverage and could handle a wide range of mutation rates. Compared with existing approaches, BHap outperformed them in terms of higher F1 scores, better precision, better recall and more accurate estimation of the number of haplotypes.

Availability And Implementation:

The BHap tool is available at http://www.cs.ucf.edu/∼xiaoman/BHap/.

Supplementary Information:

Supplementary data are available at Bioinformatics online.

More Related Videos

Using Luciferase to Image Bacterial Infections in Mice

Using Luciferase to Image Bacterial Infections in Mice

Published on: February 18, 2011

Three-Dimensional Reconstruction of Orbital Fractures

Three-Dimensional Reconstruction of Orbital Fractures

Published on: May 16, 2025

Related Concept Videos

Bacterial Signaling

Bacterial Signaling

Bacterial signaling can occur within bacteria (intracellular) or between bacteria (intercellular). At times, a group of bacteria behaves like a community. To achieve this, they engage in quorum sensing, the perception of higher cell density that causes changes in gene expression. Quorum sensing involves both extracellular and intracellular signaling. The signaling cascade starts with a molecule called an autoinducer (AI). Individual bacteria produce AIs that move out of the bacterial cell...

Bacterial Transformation

Bacterial Transformation

In 1928, bacteriologist Frederick Griffith worked on a vaccine for pneumonia, which is caused by Streptococcus pneumoniae bacteria. Griffith studied two pneumonia strains in mice: one pathogenic and one non-pathogenic. Only the pathogenic strain killed host mice.
Griffith made an unexpected discovery when he killed the pathogenic strain and mixed its remains with the live, non-pathogenic strain. Not only did the mixture kill host mice, but it also contained living pathogenic bacteria that...

Reconstruction of Signal using Interpolation

Reconstruction of Signal using Interpolation

Signal processing techniques are essential for accurately converting continuous signals to digital formats and vice versa. When a continuous signal is sampled with a period T, the resulting sampled signal exhibits replicas of the original spectrum in the frequency domain, spaced at intervals equal to the sampling frequency. To handle this sampled signal, a zero-order hold method can be applied, which creates a piecewise constant signal by retaining each sample's value until the next...

Frustration and Conflict: Approach-Approach, Approach-Avoidance

Frustration and Conflict: Approach-Approach, Approach-Avoidance

Frustration occurs when people are obstructed or prevented from achieving a desired goal or fulfilling a perceived need. For example, when someone's input is ignored in a discussion, it can lead to feelings of frustration. Conflict, however, arises from opposing interests, goals, or actions. Conflicts can take various forms based on the nature of these opposing desires or goals.
One common type of conflict is the Approach–Approach Conflict. In this case, a person faces two desirable...

Bacterial RNA Polymerase

Bacterial RNA Polymerase

Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...

Bacterial Transcription

Bacterial Transcription

RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:

Articles linked to this work by shared authors, journal, and citation graph.

Eradicating Helicobacter pylori and reversing precancerous intestinal metaplasia by gastric epithelial cells-localizable oral nanomedicines.

Bioactive materials·2026

Triazole-Triazine-Tetrazine Co-Constructed Nitrogen-Rich Covalent Organic Frameworks With Tunable H2O2 Photosynthesis and Energetic Performance by Stepwise Oxidation Strategy.

Small (Weinheim an der Bergstrasse, Germany)·2026

In vitro isolation and identification of entomopathogenic fungus (Metarhizium pinghaense) and assessment of its virulence against whiteflies and aphids.

PloS one·2026

misoTar: a novel approach for predicting miRNA and isomiR targets.

Scientific reports·2026

Engineering Ultrathin Bismuth Nanosheets With Active Facet for Highly Efficient CO2 Electroreduction to Formate.

ChemSusChem·2026

Depressive symptom trajectories around incident hip fracture in older adults: an event-centered matched analysis from the Health and Retirement Study.

Maturitas·2026

See all related articles