Foundations of Systems Biology
Using Cell Illustrator® and Pathway Databases
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Article
Open AccessLow mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks
Sharks occupy diverse ecological niches and play critical roles in marine ecosystems, often acting as apex predators. They are considered a slow-evolving lineage and have been suggested to exhibit exceptionall...
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Article
Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome
The DNA sequencing technologies in use today produce either highly accurate short reads or less-accurate long reads. We report the optimization of circular consensus sequencing (CCS) to improve the accuracy of...
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Article
Open AccessMonitoring single-cell gene regulation under dynamically controllable conditions with integrated microfluidics and software
Much is still not understood about how gene regulatory interactions control cell fate decisions in single cells, in part due to the difficulty of directly observing gene regulatory processes in vivo. We introd...
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Chapter and Conference Paper
Cell Detection with Star-Convex Polygons
Automatic detection and segmentation of cells and nuclei in microscopy images is important for many biological applications. Recent successful learning-based approaches include per-pixel cell segmentation with...
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Chapter and Conference Paper
Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks
Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconv...
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Chapter and Conference Paper
Seamless HPC Integration of Data-Intensive KNIME Workflows via UNICORE
Biological research is increasingly dependent on analyzing vast amounts of microscopy datasets. Technologies such as Fiji/ImageJ2 and KNIME support knowledge extraction from biological data by providing a larg...
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Chapter and Conference Paper
Uncertainty-Driven Forest Predictors for Vertebra Localization and Segmentation
Accurate localization, identification and segmentation of vertebrae is an important task in medical and biological image analysis. The prevailing approach to solve such a task is to first generate pixelindepen...
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Chapter and Conference Paper
Active Graph Matching for Automatic Joint Segmentation and Annotation of C. elegans
In this work we present a novel technique we term active graph matching, which integrates the popular active shape model into a sparse graph matching problem. This way we are able to combine the benefits of a glo...
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Chapter and Conference Paper
Efficient Local Alignment Discovery amongst Noisy Long Reads
Long read sequencers portend the possibility of producing reference quality genomes not only because the reads are long, but also because sequencing errors and read sampling are almost perfectly random. Howeve...
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Chapter and Conference Paper
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine
We introduce a graphical model for the joint segmentation and tracking of E. coli cells from time lapse videos. In our setup cells are grown in narrow columns (growth channels) in a so-called “Mother Machine” [1]...
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Chapter and Conference Paper
Discrete Methods for Image Analysis Applied to Molecular Biology
The field of image analysis and signal processing originally developed in the engineering community and is thus dominated by methods appealing to continuous mathematics. As a discrete mathematician recently en...
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Chapter
What’s Behind Blast
The BLAST search engine was published and released in 1990. It is a heuristic that uses the idea of a neighborhood to find seed matches that are then extended. This approach came from work that this author was...
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Article
Why bioimage informatics matters
Driven by the importance of spatial and physical factors in cellular processes and the size and complexity of modern image data, computational analysis of biological imagery has become a vital emerging sub-dis...
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Article
Open AccessAPBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010
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Chapter and Conference Paper
Automatic Recognition of Cells (ARC) for 3D Images of C. elegans
The development of high-resolution microscopy makes possible the high-throughput screening of cellular information, such as gene expression at single cell resolution. One of the critical enabling techniques ye...
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Chapter and Conference Paper
Computability of Models for Sequence Assembly
Graph-theoretic models have come to the forefront as some of the most powerful and practical methods for sequence assembly. Simultaneously, the computational hardness of the underlying graph algorithms has rem...
