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- abstractJune 2018
New features of scangraph: a tool for revealing participants' strategy from eye-movement data
ETRA '18: Proceedings of the 2018 ACM Symposium on Eye Tracking Research & ApplicationsArticle No.: 103, Pages 1–2https://doi.org/10.1145/3204493.3208334The demo describes new features of ScanGraph, an application intended for a finding of participants with a similar stimulus reading strategy based on the sequences of visited Areas of Interest. The result is visualised using cliques of a simple graph. ...
- research-articleSeptember 2015
A Normalized Parameter for Similarity/Dissimilarity Characterization of Sequences
Informatica (INFMA), Volume 26, Issue 2Pages 241–258AbstractWe propose a normalized parameter for characterization of similarity/dissimilarity of two sequences providing a smoothly varying measure for varying symmetry score. Such a parameter can be used for analysis of experimental data and fitting ...
- articleSeptember 2014
Optimizing high performance computing workflow for protein functional annotation
- Larissa Stanberry,
- Bhanu Rekepalli,
- Yuan Liu,
- Paul Giblock,
- Roger Higdon,
- Elizabeth Montague,
- William Broomall,
- Natali Kolker,
- Eugene Kolker
Concurrency and Computation: Practice & Experience (CCOMP), Volume 26, Issue 13Pages 2112–2121https://doi.org/10.1002/cpe.3264Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million ...
- articleApril 2014
Visualizing the Protein Sequence Universe
- Larissa Stanberry,
- Roger Higdon,
- Winston Haynes,
- Natali Kolker,
- William Broomall,
- Saliya Ekanayake,
- Adam Hughes,
- Yang Ruan,
- Judy Qiu,
- Eugene Kolker,
- Geoffrey Fox
Concurrency and Computation: Practice & Experience (CCOMP), Volume 26, Issue 6Pages 1313–1325https://doi.org/10.1002/cpe.3072Modern biology is experiencing a rapid increase in data volumes that challenges our analytical skills and existing cyberinfrastructure. Exponential expansion of the protein sequence universe PSU, the protein sequence space, together with the costs and ...
- research-articleJuly 2013
High performance computing workflow for protein functional annotation
XSEDE '13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to DiscoveryArticle No.: 19, Pages 1–6https://doi.org/10.1145/2484762.2484809Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the PSU (Protein Sequence Universe) expands exponentially. Newly sequenced bacterial genomes alone contain over 7.5 ...
- ArticleOctober 2012
Detecting Anomalous User Behaviors in Workflow-Driven Web Applications
SRDS '12: Proceedings of the 2012 IEEE 31st Symposium on Reliable Distributed SystemsPages 1–10https://doi.org/10.1109/SRDS.2012.19Web applications are increasingly used as portals to interact with back-end database systems and support business processes. This type of data-centric workflow-driven web application is vulnerable to two types of security threats. The first is an ...
- invited-talkJune 2012
Visualizing the protein sequence universe
- Larissa Stanberry,
- Roger Higdon,
- Winston Haynes,
- Natali Kolker,
- William Broomall,
- Saliya Ekanayake,
- Adam Hughes,
- Yang Ruan,
- Judy Qiu,
- Eugene Kolker,
- Geoffrey Fox
ECMLS '12: Proceedings of the 3rd international workshop on Emerging computational methods for the life sciencesPages 13–22https://doi.org/10.1145/2483954.2483958Modern biology is experiencing a rapid increase in data volumes that challenges our analytical skills and existing cyberinfrastructure. Exponential expansion of the Protein Sequence Universe (PSU), the protein sequence space, together with the costs and ...
- ArticleApril 2012
A Comprehensive Study about Protein Secondary Structure Based on Density Clustering
The research on protein secondary structure, which is relatively meaningful to the study of three-dimensional protein structure, has been an important topic in the area of bioinformatics. In this paper, we use a density based algorism, calculate the ...
- ArticleJuly 2009
PDSC: Clustering Object Paths from RFID Data Sets
APCIP '09: Proceedings of the 2009 Asia-Pacific Conference on Information Processing - Volume 02Pages 541–544https://doi.org/10.1109/APCIP.2009.269Radio Frequency Identification (RFID) is playing a more and more important role in our life. How to analyze and discover knowledge from RFID data sets is an urgent and challenging research field. Each tracking object will form a path when it moves ...
- ArticleJanuary 2007
Using public resource computing and systematic pre-calculation for large scale sequence analysis
High volumes of serial computational tasks in bioinformatics, such as homology searches or profile matching, are often executed in distributed environments using classical batching systems like LSF or Sun Grid-Engine. Despite their simple usability they ...
- articleMay 2006
RNA string kernels for RNAi off-target evaluation
International Journal of Bioinformatics Research and Applications (IJBRA), Volume 2, Issue 2Pages 132–146https://doi.org/10.1504/IJBRA.2006.009764RNA interference (RNAi) is a posttranscriptional gene silencing mechanism used to study gene functions, knock down viral genes, and treat diseases therapeutically. However, an 'off-target effect' deteriorates its specificity and applicability. Complete ...
- articleJanuary 2005
Multiseed Lossless Filtration
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (TCBB), Volume 2, Issue 1Pages 51–61https://doi.org/10.1109/TCBB.2005.12We study a method of seed-based lossless filtration for approximate string matching and related bioinformatics applications. The method is based on a simultaneous use of several spaced seeds rather than a single seed as studied by Burkhardt and ...