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2018 IEEE EMBS International Conference on Biomedical and Health Informatics, BHI 2018

作者： Tian, Wei Liang, Jie Bioinformatics Program Department of Bioengineering University of Illinois at Chicago ChicagoIL60607 United States

ISBN: (纸本)9781538624050

Geometric and topological features of proteins such as voids, pockets and channels are important for protein functions. We discuss a method for visualizing protein pockets and channels based on orthogonal spheres computed from alpha shapes of the protein structures, and how metric properties of channel surfaces can be mapped. In addition, we discuss how structurally prominent sites, such as constriction sties in channels, can be computed, which may help to understand protein functions and mutation effects, with implications in developing novel therapeutic interventions. © 2018 IEEE.

关键词： Proteins

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Development of a grid-based statistical potential for protein structure prediction

Development of a grid-based statistical potential for protei...

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2005 27th Annual International Conference of the Engineering in Medicine and Biology Society, IEEE-EMBS 2005

作者： Zhao, Guijun Lu, Hui Bioinformatics Program Department of Bioengineering University of Illinois at Chicago Chicago IL 60607 United States

ISBN: (纸本)0780387406

A key component in protein structure prediction is the development of potentials that can discriminate native or near native structures from the wrong ones. Most previously developed statistical potentials are based on the preferred distances between any pair of residues. Here we explore the possible angle dependence between pairs of residues in addition to their distance dependence. For simplicity, we used a grid based partition of the space and analyzed relative geometric propensity between protein residue pairs. One thousand and nine non-redundant protein structures are studied in this paper. We have attached a local coordinate system to each amino acid, and spatial distributions of its nearby residues are investigated. Within the same distance range, there are clear differences in various grids. We have further developed a grid-based statistical potential, which incorporates both the distance dependence and angle dependence using a quasi-chemical approximation. The potential is tested against 32 decoy sets, and in 25 cases the native structure has the best score. This performance is comparable and in two cases better than best performance from previously developed distance-dependent statistical potentials on residue and atom level. © 2005 IEEE.

关键词： Proteins

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BPS2025 - Probing the influence of sequence on cytotoxic and functional amyloid oligomer conformations

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Biophysical Journal 2025年第3期124卷 73a-73a页

作者： Kelsie M. King Hajar Zaheer Anne M. Brown Genetics Bioinformatics and Computational Biology Program Virginia Tech Christiansburg VA USA University of North Carolina Chapel Hill Chapel Hill NC USA Department of Biochemistry Virginia Tech University Blacksburg VA USA

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Impact of substance use disorders on critical care management and health outcomes in septic adolescents

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Annals of intensive care 2025年第1期15卷 63页

作者： Havell Markus Gary D Ceneviva Neal J Thomas Conrad Krawiec Pennsylvania State University College of Medicine 500 University Drive P.O. Box 850 Hershey PA 17033-0850 USA. hmarkus@pennstatehealth.psu.edu. Program in Bioinformatics and Genomics Pennsylvania State University Huck Life Sciences Building University Park PA 16802 USA. hmarkus@pennstatehealth.psu.edu. Medical Scientist Training Program Pennsylvania State University College of Medicine 500 University Drive Hershey PA 17033 USA. hmarkus@pennstatehealth.psu.edu. Pediatric Critical Care Medicine Department of Pediatrics Penn State Hershey Children's Hospital 500 University Drive P.O. Box 850 Hershey PA 17033-0850 USA. Department of Public Health Sciences Pennsylvania State University College of Medicine 500 University Drive Hershey PA 17033-0850 USA.

BACKGROUND:Adult septic patients with substance abuse disorder (SUD) are at increased risk of poor outcomes, but the impact on adolescents is unknown. We aimed to determine if pre-existing SUD is associated with increased adverse outcomes and critical care resources in critically ill adolescents hospitalized with sepsis. We hypothesize that SUD is associated with increased risk of adverse outcomes and usage of critical care resources in this adolescent patient population. METHODS:This was a retrospective cohort study utilizing the TriNetX© electronic health record (EHR) database, which consists of EHR from participating healthcare organizations predominantly in the United States. Critically ill adolescents with sepsis aged 12-21 years were divided into two groups (SUD history and no-SUD history). Data related to demographics, diagnostic, procedural, and medication codes were analyzed. The primary outcomes were organ dysfunction, critical care therapies, and all-cause 1-year mortality. RESULTS:We included 5,436 critically ill adolescents with sepsis [730 (13.43%) SUD history and 4706 (86.57%) no-SUD history]. SUD history was associated with increased odds of organ dysfunction (adjusted odds ratio [aOR] 1.84; 95% confidence interval [CI] 1.56-2.16; p < 0.001), vasoactive/inotropic drug usage (aOR 1.29; 95% CI 1.10-1.52; p = 0.002), mechanical ventilation (aOR 2.19; 95% CI 1.85-2.59; p < 0.001), but not mortality (aOR 1.03; 95% CI 0.76-1.41; p = 0.83). CONCLUSIONS:Our retrospective analysis suggests history of SUD in critically ill septic adolescent patients is associated with increased utilization of critical care resources and organ dysfunction. Further study is needed to determine if substance abuse represents a potentially modifiable risk factor for critical illness in adolescent patients.

关键词： Adolescent Critical care Electronic health records Substance use disorders Young adult

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A machine learning approach to resolving incongruence in molecular phylogenies and visualization analysis

A machine learning approach to resolving incongruence in mol...

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2005 IEEE Symposium on Computational Intelligence in bioinformatics and Computational Biology, CIBCB '05

作者： Xiaoxu, Han Department of Mathematics and Bioinformatics Program Eastern Michigan University Ypsilanti MI 48197 United States

ISBN: (纸本)0780393872

The incongruence between gene trees and species trees is one of the most pervasive challenges in molecular phylogenetics. In this work, a machine learning approach is proposed to overcome this problem. In the machine learning approach, the gene data set is clustered by a self-organizing map (SOM). Then a phylogenetically informative core gene set is created by combining the maximum entropy gene from each cluster to conduct phylogenetic analysis. Using the same data set, this approach performs better than the previous random gene concatenation method. The SOM based information visualization is also employed to compare the species patterns in the phylogenetic tree constructions. © 2005 IEEE.

关键词： Learning systems

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Altered protein homeostasis in cardiovascular diseases contributes to Alzheimer's-like neuropathology

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Basic research in cardiology 2025年 2025 May 7页

作者： Nirjal Mainali Meenakshisundaram Balasubramaniam Sonu Pahal W Sue T Griffin Robert J Shmookler Reis Srinivas Ayyadevara Bioinformatics Program University of Arkansas for Medical Sciences and University of Arkansas at Little Rock Little Rock AR 72205 USA. Department of Geriatrics Reynolds Institute on Aging University of Arkansas for Medical Sciences Little Rock AR 72205 USA. Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA. Central Arkansas Veterans Healthcare Service Little Rock AR 72205 USA. ayyadevarasrinivas@uams.edu. Department of Geriatrics Reynolds Institute on Aging University of Arkansas for Medical Sciences Little Rock AR 72205 USA. ayyadevarasrinivas@uams.edu.

Cardiovascular diseases (CVDs) are the leading cause of death worldwide. CVD is known to increase the risk of subsequent neurodegeneration but the mechanism(s) and proteins involved have yet to be elucidated. We previously showed that myocardial infarction (MI), induced in mice and compared to sham-MI mice, leads to increases in protein aggregation, endoplasmic reticulum (ER) stress in both heart and brain, and changes in proteostatic pathways. In this study, we further investigate the molecular mechanisms altered by induced MI in mice, which were also implicated by proteomics of postmortem human hippocampal aggregates from Alzheimer's disease (AD) and cardiovascular disease (CVD) patients, vs. age-matched controls (AMC). We utilized intra-aggregate crosslinking to identify protein-protein contacts or proximities, and thus to reconstruct aggregate "contactomes" (nonfunctional interactomes). We used leave-one-out analysis (LOOA) to determine the contribution of each protein to overall aggregate cohesion, and gene ontology meta-analyses of constituent proteins to define critical organelles, processes, and pathways that distinguish AD and/or CVD from AMC aggregates. We identified influential proteins in both AD and CVD aggregates, many of which are associated with pathways or processes previously implicated in neurodegeneration such as mitochondrial, oxidative, and endoplasmic-reticulum stress; protein aggregation and proteostasis; the ubiquitin proteasome system and autophagy; axonal transport; and synapses.

关键词： Alzheimer’s disease Cardiovascular disease Crosslinking studies Leave-one-out analysis Protein aggregates

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Finding phylogenetically informative genes by estimating multispecies gene entropy

Finding phylogenetically informative genes by estimating mul...

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International Joint Conference on Neural Networks 2006, IJCNN '06

作者： Xiaoxu, Han Department of Mathematics Bioinformatics Program Eastern Michigan University Ypsilanti MI 48197 United States

ISBN: (纸本)0780394909

Although entropy and relative entropy (K-L distance) are widely applied in many bioinformatics areas, there is no method given to compute the multispecies gene entropy yet. This paper presents the first multispecies gene entropy estimation method from the data mining point of view. In this study, a self-organizing map (SOM) is employed to mine a multispecies gene set to obtain the probability distribution of each gene in the feature space, which is the approximation of its corresponding probability distribution in the original sequence space. The multispecies gene entropy is computed by the probability distribution of a gene in the feature space. The phylogenetic applications of the multispecies gene entropy are investigated in an example of resolving incongruence between gene trees and species trees. It is found that genes with nearest K-L distances to the minimum entropy gene are more likely to be phylogenetically informative. A K-L distance based gene concatenation approach under gene clustering is proposed to resolve the gene tree and species tree problem. Under the same testing dataset, the K-L distance based approach not only avoids the ad-hoc mechanism of the original gene concatenation method but also is easy to extend to other dataset and free from prohibitive phylogenetic computing from large number of taxa. © 2006 IEEE.

关键词： Gene expression

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The SinBiota 2.0 biodiversity information system

The SinBiota 2.0 biodiversity information system

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7th IEEE International Conference on eScience, eScience 2011

作者： Mira, Cleber Feijao, Pedro Duque-Estrada, Tiago Meidanis, Joao Joly, Carlos A. BIOTA-FAPESP Program Brazil University of Campinas Campinas Brazil Scylla Bioinformatics Campinas Brazil

ISBN: (纸本)9780769545974

For the last 10 years, Sin Biota, the information system of the Biota-FAPESP program, has served the community storing and displaying data in maps, and providing a common base for researchers in different areas to communicate and exchange biodiversity data. State administration has also used the system to support new laws and regulations. Now it is time to rethink the system, which has grown in an ad-hoc, unstructured way, aiming at the support that will be needed for the next 10 years. In a project jointly funded by Microsoft Research and FAPESP, we aim at the creation of a specification for the new Sin Biota 2.0 system, including cutting-edge services and technologies on information technology, in order to achieve a number of goals, namely: guarantee the use and expansion of the system for the next ten years, support the availability of a larger volume of higher quality environmental data, oriented also to the educational and public administration sectors, provide more efficient sharing of data among BIOTA researchers, inter-operate with international initiatives, provide effective tools to assist researchers in finding relevant information amongst a large amount of environment data. The expected results at the end of this project are the composition of a specification (Reference Document) of the Sin Biota 2.0 system, and the implementation of a prototype that will gradually replace the current system. We propose in this work the system architecture and our vision of the main features that would allow Sin Biota 2.0 to meet the expectations of the biodiversity research community and other stakeholders. We also describe a prototype application that implements most of the features present in the current Sin Biota 1.0 system, as well as some of the new features envisaged for the new version. © 2011 IEEE.

关键词： Biodiversity

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Modeling and analyzing three-dimensional structures of human disease proteins

Modeling and analyzing three-dimensional structures of human...

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11th Pacific Symposium on Biocomputing 2006, PSB 2006

作者： Ye, Yuzhen Li, Zhanwen Godzik, Adam Bioinformatics and Systems Biology Program Burnham Institute San Diego CA 92037 United States

ISBN: (纸本)9812564632

Three-dimensional structures of proteins, experimental or predicted, show us how these molecular machines actually work. With the help of information on disease-related mutations, they can also show us how they malfunction in diseases. Such understanding, currently lacking for most human diseases, is an important first step before designing drugs or therapies to cure specific diseases. Here we used homology modeling to model human disease-related proteins, and studied structural characteristics of disease related' mutations and compared them with non synonymous SNPs. 1484 domains from 874 proteins were modeled, and together with experimentally determined structures of 369 domains they provided the structural coverage of 48% of total residues in 1237 human disease proteins. We found that disease-related mutations have statistically significantly preference to form clusters on protein surfaces. In contrast, the non-synonymous SNPs appear to be randomly distributed on the surface. We interpret these results as an indication that disease mutations affect protein-protein interaction interfaces. This interpretation is supported by the analysis of 8 experimentally determined complexes between disease proteins, where disease-related mutations are clearly located in the binding interface of proteins, while SNPs are not. The non-uniform distribution of disease mutations indicates that we can use this feature as guidance in modeling and evaluating human disease proteins and their complexes. We set up a resource for Disease Protein Models (DPM at http://***/DPM>. which can be used for studying the relation between disease and mutation / polymorphism sites in the context of protein 3D structures and complexes.

关键词： Proteins

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Comparative analysis of gene regulation in single cells using Compass

Cell reports methods

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Cell reports methods 2025年第5期5卷 101035页

作者： Changxin Wan Yilong Qu Zhiyou Ye Tianbei Zhang Huifang Ma Ming Chen Wenpin Hou Zhicheng Ji Department of Biostatistics and Bioinformatics Duke University School of Medicine Durham NC USA Program of Computational Biology and Bioinformatics Duke University School of Medicine Durham NC USA. Department of Biostatistics and Bioinformatics Duke University School of Medicine Durham NC USA. Department of Biomedical Engineering Pratt School of Engineering Duke University Durham NC USA. Department of Pathology Duke University School of Medicine Durham NC USA Duke Cancer Institute Duke University Durham NC USA. Department of Biostatistics Columbia University Mailman School of Public Health New York City NY USA. Program of Computational Biology and Bioinformatics Duke University School of Medicine Durham NC USA. Electronic address: zhicheng.ji@duke.edu.

Single-cell multi-omics is a transformative technology that measures both gene expression and chromatin accessibility in individual cells. However, most studies concentrate on a single tissue and are unable to determine whether a gene is regulated by a cis-regulatory element (CRE) in just one tissue or across multiple tissues. We developed Compass for comparative analysis of gene regulation across a large number of human and mouse tissues. Compass consists of a database, CompassDB, and an open-source R software package, CompassR. CompassDB contains processed single-cell multi-omics data of more than 2.8 million cells from hundreds of cell types. Building upon CompassDB, CompassR enables visualization and comparison of gene regulation across multiple tissues. We demonstrated that CompassR can identify CRE-gene linkages specific to a tissue type and their associated transcription factors in real examples.

关键词： CP: Systems biology cis-regulatory elements gene regulation single-cell ATAC-seq single-cell multi-omics

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