Open Access. Powered by Scholars. Published by Universities.®
- Institution
- Keyword
-
- Data representation (15)
- Robert Hooke (15)
- Scientific imaging (15)
- Ab initio protein structure predictions (1)
- Bioinformatics (1)
-
- Biomedical engineering (1)
- Cryo-electron microscopy (cryo-EM) (1)
- Density maps (1)
- Electron Microscopy Data Bank (EMDB) (1)
- F1 scores (1)
- Genome assembly (1)
- Helix (1)
- Human subtelomeric regions (1)
- Linked-reads (1)
- Museum Exhibit Insulation (1)
- NPGREAT (1)
- Nanopore reads (1)
- Performance computing (1)
- Quark (1)
- REXTAL (1)
- Resolution (1)
- Subtelomeres (1)
- Telomeres (1)
- TrRosetta (1)
Articles 1 - 23 of 23
Full-Text Articles in Computer Sciences
Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He
Analysis Of Ab Initio Protein Structure Prediction Methods, Maytha Alshammari, Jing He
College of Sciences Posters
Protein structure prediction produces atomic models of three-dimensional structure of a protein from its amino acid sequence. Understanding the function mechanism of proteins requires knowledge of three-dimensional structures. When developing new enzymes and drugs, it's essential to understand the structure of the target protein. In this study, we analyze models predicted using two ab initio protein structure prediction methods, trRosetta and Quark. A set of thirty protein chains was used to evaluate the effectiveness of the methods. The thirty chains were collected from Protein Data Bank (June – November, 2020). The length and the relative position of the predicted secondary …
Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman
Nanopore Guided Regional Assembly, Eleni Adam, Desh Ranjan, Harold Riethman
College of Sciences Posters
The telomeres are the “caps” of the chromosomes and their vital role is to protect them. Possible telomere dysfunction caused by telomere rearrangements can be fatal for the cell and result in age-related diseases, including cancer. The telomeres and subtelomeres are regions that are hard to investigate. The current technology cannot provide their complete sequence, instead the DNA is given in multiple pieces. Current methods of assembling the pieces of these regions are not accurate enough due to the region’s high variability and complex repeated patterns. We propose a hybrid assembly method, the NPGREAT, which utilizes two of the latest …
Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman
Npgreat: Hybrid Assembly Of Human Subtelomeres With The Use Of Nanopore And Linked-Read Datasets, Eleni Adam, Desh Ranjan, Harold Riethman
College of Sciences Posters
The telomeres are vitally important regions that are located at the tips of the chromosomes. Their dysfunction, caused by length shortening can lead to senescent cells, which in turn cause age-related diseases, including cancer. The subtelomeres, located next to the telomeres, possess the critical role of regulating the adjacent telomere lengths. Even after many years of research, human subtelomeres have proven to be very hard to assemble due to their morphology. In order to overcome these problems, the hybrid assembly method we develop utilizes two of the latest available types of data, which complement each other: Linked-Reads and ultralong Nanopore …
Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer
Multi-Label Model For Toxicity Prediction, Xiu Huan Yap, Michael L. Raymer
Symposium of Student Research, Scholarship, and Creative Activities Materials
Most computational predictive models are specifically trained for a single toxicity endpoint. Since more than 1300 toxicity assays have been reported in the TOXCAST dashboard, achieving high coverage over this growing number of toxicity endpoints remains challenging. Furthermore, single-endpoint models lack the ability to learn dependencies between endpoints, such as those targeting similar biological pathways, which may be used to boost model performance. In this study, we characterize the performance of 3 multi-label classification (MLC) models, namely Classifier Chains (CC), Label Powersets (LP) and Stacking (SBR), on Tox21 challenge data. These MLC models employ the Problem Transformation approach, which is …
Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He
Cylindrical Similarity Measurement For Helices In Medium-Resolution Cryo-Electron Microscopy Density Maps, Salim Sazzed, Peter Scheible, Maytha Alshammari, Willy Wriggers, Jing He
College of Sciences Posters
Cryo-electron microscopy (cryo-EM) density maps at medium resolution (5-10 Å) reveal secondary structural features such as α-helices and β-sheets, but they lack the side chains details that would enable a direct structure determination. Among the more than 800 entries in the Electron Microscopy Data Bank (EMDB) of medium-resolution density maps that are associated with atomic models, a wide variety of similarities can be observed between maps and models. To validate such atomic models and to classify structural features, a local similarity criterion, the F1 score, is proposed and evaluated in this study. The F1 score is theoretically normalized to a …
Statistical Analysis Of Social Network Change, Teresa D. Schmidt
Statistical Analysis Of Social Network Change, Teresa D. Schmidt
Systems Science Friday Noon Seminar Series
We explore two statistical methods that infer social network structures and statistically test those structures for change over time: regression-based differential network analysis (R-DNA) and information theory-based differential network analysis (I-DNA). RDNA is adapted from bioinformatics and I-DNA employs reconstructability analysis. Both methods are used to analyze Medicaid claims data from one-year periods before and after the formation of the Health Share of Oregon Coordinated Care Organization (CCO). We hypothesized that Health Share’s CCO formation would be followed by several changes in the healthcare delivery network.
Application of R-DNA and I-DNA to claims data involves three steps: (a) the inference …
Bioinformatics And Biomedical Engineering, Francisco Ortuño, Ignacio Rojas, Kathryn Dempsey Cooper, Sachin Pawaskar, Hesham Ali
Bioinformatics And Biomedical Engineering, Francisco Ortuño, Ignacio Rojas, Kathryn Dempsey Cooper, Sachin Pawaskar, Hesham Ali
Faculty Books and Monographs
Editors: Francisco Ortuño, Ignacio Rojas
Chapter, Identification of Biologically Significant Elements Using Correlation Networks in High Performance Computing Environments, co-authored by Kathryn Dempsey Cooper, Sachin Pawaskar, and Hesham Ali, UNO faculty members.
The two volume set LNCS 9043 and 9044 constitutes the refereed proceedings of the Third International Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, held in Granada, Spain in April 2015. The 134 papers presented were carefully reviewed and selected from 268 submissions. The scope of the conference spans the following areas: bioinformatics for healthcare and diseases, biomedical engineering, biomedical image analysis, biomedical signal analysis, computational genomics, computational …
Conclusion Panel, Allison Marsh
Usc's Nanocenter, Allison Marsh
Usc's Nanocenter, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Fact Or Fiction?, Allison Marsh
Fact Or Fiction?, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Nano Imaging, Allison Marsh
Nano Imaging, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Choosing An Instrument, Allison Marsh
Choosing An Instrument, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
A Crossword Puzzle For Kids, Allison Marsh
An Exhibit Wordle, Allison Marsh
Word Find, Allison Marsh
Lesson Plans, Activities, And Further Reading, Allison Marsh
Lesson Plans, Activities, And Further Reading, Allison Marsh
Handouts
No abstract provided.
Images From The Exhibit, Page 2, Allison Marsh
Images From The Exhibit, Page 1, Allison Marsh
Title Panel, Allison Marsh
What Is Nanotechnology?, Allison Marsh
What Is Nanotechnology?, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Spotlight On Usc: Department Of Art, Allison Marsh
Spotlight On Usc: Department Of Art, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Art Versus Image, Allison Marsh
Art Versus Image, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.
Nanotechnology In Everyday Life, Allison Marsh
Nanotechnology In Everyday Life, Allison Marsh
Section 5: Imaging at the Nano Scale
No abstract provided.