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第十七届国际生物物理大会;第十二届中国生物物理大会

作者： Santhosh K.Vammi Department of Computer Sciece Program of Bioinformatics and Computational biologyIowa State UniversityAmesIowaUSA

Ensembles have been increasingly used to represent the heterogeneity of protein native states and there is a number of exciting recent work that determines such ensembles using experimental *** what extent these ensembles represent the native states is debatable since the ensemble,which may contain over a hundred conformations,may be underconstrained by the experimental *** this work,we introduce a new feature,the

关键词： structure ensemble conformation states populations ubiquitin dynamics

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Admixture mapping analysis in the context of GWAS with GAW18 data

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BMC proceedings 2014年第Suppl 1期8卷 S3页

作者： Mengjie Chen Can Yang Cong Li Lin Hou Xiaowei Chen Hongyu Zhao Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA. Department of Biostatistics Yale School of Public Health Yale University New Haven CT 06520 USA. Program in Computational Biology and Bioinformatics Yale University New Haven CT 06520 USA

Admixture mapping is a disease-mapping strategy to identify disease susceptibility variants in an admixed population that is a result of mating between 2 historically separated populations differing in allele frequencies and disease prevalence. With the increasing availability of high-density genotyping data generated in genome-wide association studies, it is of interest to investigate how to apply admixture mapping in the context of the genome-wide association studies and how to adjust for admixture in association tests. In this study, we first evaluated 3 different local ancestry inference methods, LAMP, LAMP-LD, and MULTIMIX. Then we applied admixture mapping analysis based on estimated local ancestry. Finally, we performed association tests with adjustment for local ancestry.

关键词： Reference Panel Admixture Mapping Local Ancestry Native American Ancestry Human Genome Diversity Project

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Disagreement in middle ear volume estimation between tympanometry and three-dimensional volume reconstruction in the context of tympanic membrane perforation

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Journal of Otology 2017年第2期12卷 74-79页

作者： David J.Carpenter Debara L.Tucci David M.Kaylie Dennis O.Frank-Ito Division of Head and Neck Surgery&Communication Sciences Department of SurgeryDuke University Medical CenterDurhamNCUSA Computational Biology&Bioinformatics PhD Program Duke UniversityDurhamNCUSA Department of Mechanical Engineering and Materials Science Duke UniversityDurhamNCUSA

Introduction: Middle ear volume(MEV) is a clinically relevant parameter across middle ear diseases. MEV values between these techniques have never before been tested for agreement in ears with perforated tympanic membranes(TMs).Methods: Middle ears were identified from 36 patients ranging 18-89 years of age with TM perforations who underwent tympanometry and temporal bone computed tomography(CT) between 2005 and 2015. MEVs calculated by both tympanometry and three-dimensional volume reconstruction(3DVR) were analyzed for agreement using Bland Altman plots. The differences between tympanometric and 3DVR MEV values for each given middle ear were characterized across MEV quartiles(1= smallest; 4= largest) and across increasing states of middle ear disease using Kruskale Wallis and Wilcoxon testing with Bonferroni ***: Bland Altman plots demonstrated significant disagreement between MEV measurement techniques. Differences between tympanometric(T) and 3DVR MEV values were significantly greater with increasing average(i.e.(Tt3DVR)/2)) MEV per linear regression(p < 0.0001). Significance was demonstrated between fourth and first average MEV quartiles(p= 0.0024), fourth and second quartiles(p= 0.0024), third and first quartiles(p= 0.0048), and third and second quartiles(p= 0.048). Absolute MEV difference was not significantly different across varying states of middle ear disease(p= 0.44).Conclusion: Statistically and clinically significant disagreement was demonstrated between tympanometric and 3DVR MEV values. Studies that vary in MEV estimation techniques may be expected to demonstrate significantly different results. These preliminary results suggest that clinicians should endeavor to seek further confirmation when interpreting high tympanometric MEV values.

关键词： Middle ear volume Tympanometry Three-dimensional volume reconstruction Tympanic membrane perforation

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Identification of novel TMEM16A blockers through integrated virtual screening, molecular dynamics, and experimental studies

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Scientific Reports 2025年第1期15卷 1-11页

作者： Sangkhawasi, Mattanun Pitaktrakul, Wichuda Khumjiang, Rungtiwa Shigeta, Yasuteru Muanprasat, Chatchai Hengphasatporn, Kowit Rungrotmongkol, Thanyada Center of Excellence in Biocatalyst and Sustainable Biotechnology Department of Biochemistry Faculty of Science Chulalongkorn University Bangkok 10330 Thailand Chakri Naruebodindra Medical Institute Faculty of Medicine Ramathibodi Hospital Mahidol University Bang Pla Bang Pli Samut Prakan 10540 Thailand Division of Biochemistry Department of Preclinical Science Faculty of Medicine Thammasat University Pathumthani 12120 Thailand Center for Computational Sciences University of Tsukuba 1-1-1 Tennodai Ibaraki Tsukuba 305-8577 Japan Program in Bioinformatics and Computational Biology Graduate School Chulalongkorn University Bangkok 10330 Thailand

The calcium-activated chloride channel TMEM16A is a promising drug target for treating hypertension, secretory diarrheas, and various cancers, including head and neck cancer. Despite its potential, no FDA-approved drugs have provided the structural basis for directly inhibiting TMEM16A. This study aims to identify a novel pore-blocker of TMEM16A by integrating virtual screening, molecular dynamics simulations, and in vitro studies. Using the calcium-bound structure of TMEM16A with and without the pore-blocker 1PBC, we performed virtual screening on nearly 90,000 compounds from the ChemDiv database. Approximately 67% of these compounds demonstrated better binding affinity than 1PBC. Among the top 20 compounds selected for short-circuit current assays using human lung adenocarcinoma cells (Calu-3), compounds N066-0059, N066-0060, and N066-0067 inhibited TMEM16A activity with IC50 values of 0.24 µM, 0.41 µM, and 0.48 µM, respectively, which was lower than that of a positive control Ani9 (9 µM). Due to its highest potency in electrophysiological assays, N066-0059 was subjected to mechanistic studies. Molecular dynamics simulations elucidated its binding stability and strength, showing superior performance to 1PBC over 500 ns with 3 replicates. This study advances TMEM16A-targeted drug development, offering new insights for anticancer therapies. © The Author(s) 2025.

关键词： And electrophysiological assays Cytotoxicity Molecular dynamics Pore-blocker inhibitor TMEM16A Virtual screening

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Geometry based data generation 32

Geometry based data generation

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32nd Conference on Neural Information Processing Systems, NeurIPS 2018

作者： Lindenbaum, Ofir Wolf, Guy Stanley, Jay S. Krishnaswamy, Smita Applied Mathematics Program Yale University New HavenCT06511 United States Computational Biology and Bioinformatics Program Yale University New HavenCT06510 United States Departments of Genetics and Computer Science Yale University New HavenCT06510 United States

We propose a new type of generative model for high-dimensional data that learns a manifold geometry of the data, rather than density, and can generate points evenly along this manifold. This is in contrast to existing generative models that represent data density, and are strongly affected by noise and other artifacts of data collection. We demonstrate how this approach corrects sampling biases and artifacts, thus improves several downstream data analysis tasks, such as clustering and classification. Finally, we demonstrate that this approach is especially useful in biology where, despite the advent of single-cell technologies, rare subpopulations and gene-interaction relationships are affected by biased sampling. We show that SUGAR can generate hypothetical populations, and it is able to reveal intrinsic patterns and mutual-information relationships between genes on a single-cell RNA sequencing dataset of hematopoiesis. © 2018 Curran Associates Inc..All rights reserved.

关键词： Genes

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Influence of conformational change of chain unit on the intrinsic negative thermal expansion of polymers

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Chinese Chemical Letters 2021年第4期32卷 1515-1518页

作者： Qiangsheng Sun Ke Jin Yuhui Huang Jia Guo Thanyada Rungrotmongkol Phornphimon Maitarad Changchun Wang State Key Laboratory of Molecular Engineering of Polymers and Department of Macromolecular Science Fudan UniversityShanghai 200433.China Biocatalyst and Environmental Biotechnology Research Unit Department of BiochemistryFaculty of Science and Program in Bioinformatics and Computational BiologyGraduate SchoolChulalongkom UniversityBangkok 10330Thailand Research Center of Nano Science and Technology Shanghai UniversityShanghai 200444China

Negative thermal expansion(NTE) behavior has roused wide interest for the control of thermomechanical properties of functional *** NTE behaviors have been found in kinds of compounds,it remains challenging for polymers to achieve intrinsic NTE *** this work,we systematically studied the conformational change of dibenzocyclooctadiene(DBCOD) derivatives between chair(C) and twist-boat(TB) forms based on density-functional theo ry(DFT) calculations,and found clear evidence of the relationship between the structure of DBCOD units and the thermal contraction behavior of the related *** order to obtain the polymer with NTE property,two conditions should be met for the thermal contracting DBCOD related units as follows:(i) the TB conformation can turn into C conformation as the temperature increases,and(ii) the volume of C conformation is smaller than that of TB *** rule should offer a guidance to exploration of the new intrinsic NTE polymers in the future.

关键词： Negative thermal expansion Conformational change Polyarylamides Density-functional theory Dibenzocyclooctadiene

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CoreGenes3.5: A webserver for the determination of core genes from sets of viral and small bacterial genomes

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BMC Research Notes 2013年第1期6卷 1-4页

作者： Turner, Dann Reynolds, Darren Seto, Donald Mahadevan, Padmanabhan Centre for Research in Biosciences Faculty of Applied Sciences University of the West of England Bristol BS16 1QY United Kingdom Bioinformatics and Computational Biology Program School of Systems Biology George Mason University Manassas VA 20110 United States Department of Biology University of Tampa Tampa FL 33606 United States

Background: CoreGenes3.5 is a webserver that determines sets of core genes from viral and small bacterial genomes as an automated batch process. Previous versions of CoreGenes have been used to classify bacteriophage genomes and mine data from pathogen genomes. Findings. CoreGenes3.5 accepts as input GenBank accession numbers of genomes and performs iterative BLASTP analyses to output a set of core genes. After completion of the program run, the results can be either displayed in a new window for one pair of reference and query genomes or emailed to the user for multiple pairs of small genomes in tabular format. Conclusions: With the number of genomes sequenced increasing daily and interest in determining phylogenetic relationships, CoreGenes3.5 provides a user-friendly web interface for wet-bench biologists to process multiple small genomes for core gene determinations. CoreGenes3.5 is available at. © 2013 Turner et al.;licensee BioMed Central Ltd.

关键词： Bacteriophage Core genes Data mining Taxonomy Viral genomics

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Manifold learning-based methods for analyzing single-cell RNA-sequencing data

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Current Opinion in Systems biology 2018年 7卷 36-46页

作者： Moon, Kevin R. Stanley, Jay S. Burkhardt, Daniel van Dijk, David Wolf, Guy Krishnaswamy, Smita Department of Genetics Yale University New Haven CT United States Applied Mathematics Program Yale University New Haven CT United States Computational Biology and Bioinformatics Program Yale University New Haven CT United States Department of Computer Science Yale University New Haven CT United States

Recent advances in single-cell RNA sequencing technologies enable deep insights into cellular development, gene regulation, and phenotypic diversity by measuring gene expression for thousands of cells in a single experiment. While these technologies hold great potential for improving our understanding of cellular states and progression, they also pose new challenges and require advanced mathematical and algorithmic tools to extract underlying biological signals. In this review, we cover one of the most promising avenues of research into unlocking the potential of scRNA-seq data: the field of manifold learning, and the related manifold assumption in data analysis. Manifold learning provides a powerful structure for algorithmic approaches to process the data, extract its dynamics, and infer patterns in it. In particular, we cover manifold learning-based methods for denoising the data, revealing gene interactions, extracting pseudotime progressions with model fitting, visualizing the cellular state space via dimensionality reduction, and clustering the data. © 2017 Published by Elsevier Ltd.

关键词： Data mining Gene regulatory networks Imputation Manifold learning Pseudotime trends Single cell RNA sequencing

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Parsimonious reconstruction of network evolution

Parsimonious reconstruction of network evolution

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Lecture Notes in Computer Science

作者： Patro, Rob Sefer, Emre Malin, Justin Marçais, Guillaume Navlakha, Saket Kingsford, Carl Center for Bioinformatics and Computational Biology University of Maryland College Park MD 20742 United States Department of Computer Science University of Maryland College Park MD 20742 United States Computational Biology Bioinformatics and Genomics Concentration Biological Sciences Graduate Program University of Maryland College Park MD 20742 United States Program in Applied Mathematics Statistics and Scientific Computation University of Maryland College Park MD 20742 United States School of Computer Science Carnegie Mellon University Pittsburgh PA 15213 United States

ISBN: (纸本)9783642230370

We consider the problem of reconstructing a maximally parsimonious history of network evolution under models that support gene duplication and loss and independent interaction gain and loss. We introduce a combinatorial framework for encoding network histories, and we give a fast procedure that, given a set of duplication histories, in practice finds network histories with close to the minimum number of interaction gain or loss events. In contrast to previous studies, our method does not require knowing the relative ordering of unrelated duplication events. Results on simulated histories suggest that common ancestral networks can be accurately reconstructed using this parsimony approach. © 2011 Springer-Verlag.

关键词： Genes

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Conservation of ancient full-length open reading frames in vertebrate endogenous retroviruses

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Retrovirology 2011年第2期8卷 1-2页

作者： Hugo Martins Palle Villesen Bioinformatics Research Centre Aarhus University Denmark PhD Program in Computational Biology Instituto Gulbenkian de Ciências Oeiras Portugal

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