SelectedWorks - William B. Andreopoulos

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Selected Works of William B. Andreopoulos

Assistant Professor, Department of Computer Science

William B. Andreopoulos is a Assistant Professor in the Department of Computer Science at San José State University.

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About William B. Andreopoulos

William B. Andreopoulos is a Assistant Professor in the Department of Computer Science at San José State University.

The Melampsora americana Population on Salix purpurea in the Great ...

Phytopathology (2022)

Chase R. Crowell, Dustin G. Wilkerson, Mariami Beckauri, Ali R. Cala, et al.

Shrub willows (Salix spp.) are emerging as a viable lignocellulosic, second-generation bioenergy crop with many growth characteristics favorable for marginal ...

Deeplasmid: Deep learning accurately separates plasmids from bacterial chromosomes

Nucleic Acids Research (2022)

William B. Andreopoulos, Alexander M. Geller, Miriam Lucke, Jan Balewski, et al.

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of ...

The extracellular contractile injection system is enriched in environmental microbes ...

Nature Communications (2021)

Alexander Martin Geller, Inbal Pollin, David Zlotkin, Aleks Danov, et al.

The extracellular Contractile Injection System (eCIS) is a toxin-delivery particle that evolved from a bacteriophage tail. Four eCISs have previously ...

Prediction of higher-order links using global vectors and Hasse diagrams

Proceedings - 2021 IEEE International Conference on Big Data, Big Data 2021 (2021)

Kalpnil Anjan, Willam Andreopoulos and Katerina Potika

The primary objective of this work is to utilize the GloVeNoR node embedding technique, as well as the Simplex2Vec triangle ...

Convolutional neural networks and extreme learning machines for malware classification

Journal of Computer Virology and Hacking Techniques (2020)

Mugdha Jain, William Andreopoulos and Mark Stamp

Research in the field of malware classification often relies on machine learning models that are trained on high-level features, such ...

Draft Genome Sequences of Three Monokaryotic Isolates of the White-Rot ...

Microbiology Resource Announcements (2019)

Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, et al.

Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes ...

Megaphylogeny Resolves Global Patterns of Mushroom Evolution

Nature Ecology & Evolution (2019)

Torda Varga, Krisztina Krizsán, Csenge Földi, Bálint Dima, et al.

Mushroom-forming fungi (Agaricomycetes) have the greatest morphological diversity and complexity of any group of fungi. They have radiated into most ...

Leveraging Single-cell Genomics to Expand the Fungal Tree of Life

Nature Microbiology (2018)

Steven R. Ahrendt, C. Alisha Quandt, Doina Ciobanu, Alicia Clum, et al.

Environmental DNA surveys reveal that most fungal diversity represents uncultured species. We sequenced the genomes of eight uncultured species across ...

Widespread Adenine N6-methylation of Active Genes in Fungi

Nature Genetics (2017)

Stephen J . Mondo, Richard O. Dannebaum, Rita C. Kuo, Katherine B. Louie, et al.

N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes1,2,3,4, but its prevalence ...

Clustering Categorical Data

Wiley StatsRef: Statistics Reference Online (2017)

Bill Andreopoulos

A growing number of clustering algorithms for categorical data have been proposed. This article describes the goals of clustering categorical ...

Next Generation Sequencing Data of a Defined Microbial Mock Community

Scientific Data (2016)

Esther Singer, Bill Andreopoulos, Robert M. Bowers, Janey Lee, et al.

Generating sequence data of a defined community composed of organisms with complete reference genomes is indispensable for the benchmarking of ...

Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific ...

Cancer Informatics (2012)

Bill Andreopoulos and Dimitris Anastassiou

Gene expression profiling has provided insights into different cancer types and revealed tissue-specific expression signatures. Alterations in microRNA expression contribute ...

Efficient Unfolding Pattern Recognition in Single Molecule Force Spectroscopy Data

Algorithms for Molecular Biology (2011)

Bill Andreopoulos and Dirk Labudde

BackgroundSingle-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance ...

Triangle Network Motifs Predict Complexes By Complementing High-error Interactomes With ...

BMC Bioinformatics (2009)

Bill Andreopoulos, Christof Winter, Dirk Labudde and Michael Schroeder

BackgroundA lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, ...

A Roadmap of Clustering Algorithms: Finding a Match for a ...

Briefings in Bioinformatics (2009)

Bill Andreopoulos, Aijun An, Xiaogang Wang and Michael Schroeder

Clustering is ubiquitously applied in bioinformatics with hierarchical clustering and k-means partitioning being the most popular methods. Numerous improvements of ...

Efficient Layered Density-based Clustering of Categorical Data

Journal of Biomedical Informatics (2009)

Bill Andreopoulos, Aijun An, Xiaogang Wang and Dirk Labudde

A challenge involved in applying density-based clustering to categorical biomedical data is that the ”cube” of attribute values has no ...

Biomedical Word Sense Disambiguation With Ontologies And Metadata: Automation Meets ...

BMC Bioinformatics (2009)

Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, et al.

BackgroundOntology term labels can be ambiguous and have multiple senses. While this is no problem for human annotators, it is ...

Contribution to Book

Promoting Diversity in Top Hits for Biomedical Passage Retrieval

Advances in Data Management (2009)

Bill Andreopoulos, Xiangji Huang, Aijun An, Dirk Labudde, et al.

With the volume of biomedical literature exploding, such as BMC or PubMed, it is of paramount importance to have scalable ...

Word Sense Disambiguation in Biomedical Ontologies With Term Co-occurrence Analysis ...

International Journal of Data Mining and Bioinformatics (2008)

Bill Andreopoulos, Dimitra Alexopoulou and Michael Schroeder

With more and more genomes being sequenced, a lot of effort is devoted to their annotation with terms from controlled ...

Unraveling Protein Networks with Power Graph Analysis

PLoS Computational Biology (2008)

Loïc Royer, Matthias Reimann, Bill Andreopoulos and Michael Schroeder

Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph ...

Clustering by Common Friends Finds Locally Significant Proteins Mediating Modules

Bioinformatics (2007)

Bill Andreopoulos, Aijun An, Xiaogang Wang, Michalis Faloutsos, et al.

Motivation: Much research has been dedicated to large-scale protein interaction networks including the analysis of scale-free topologies, network modules and ...

Clustering Large Software Systems at Multiple Layers

Information and Software Technology (2007)

Bill Andreopoulos, Aijun An, Vassilios Tzerpos and Xiaogang Wang

Software clustering algorithms presented in the literature rarely incorporate in the clustering process dynamic information, such as the number of ...

Finding Molecular Complexes Through Multiple Layer Clustering of Protein Interaction ...

International Journal of Bioinformatics Research and Applications (2007)

Bill Andreopoulos, Aijun An, Xiangji Huang and Xiaogang Wang

Clustering protein-protein interaction networks (PINs) helps to identify complexes that guide the cell machinery. Clustering algorithms often create a flat ...

Bi-level Clustering of Mixed Categorical and Numerical Biomedical Data

International Journal of Data Mining and Bioinformatics (2006)

Bill Andreopoulos, Aijun An and Xiaogang Wang

Biomedical data sets often have mixed categorical and numerical types, where the former represent semantic information on the objects and ...

Contribution to Book

Protein-Protein Interaction Networks

Protein Purification and Analysis I: Methods and Applications (2013)

Bill Andreopoulos and Dirk Labudde