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IEEE Data Science Workshop (DSW)

作者： Daniel B. Burkhardt Jay S. Stanley III Guy Wolf Smita Krishnaswamy Department of Genetics Computational Biology and Bioinformatics Program Department of Mathematics and Statistics Université de Montréal

We propose a novel approach for clustering the vertices of a graph. The method, Vertex-Frequency Clustering (VFC), considers the local harmonic content of one or many graph signals, forming partitions based on spectral features in the input signal. The method can be related to spectral clustering, and the length scale over which frequencies are considered is tunable. This allows one to cluster data based on intrinsic graph geometry in the context of signal dynamics. VFC is useful for unravelling active regions in a signal, collecting sets of similar observations, or detecting anomalies. We demonstrate the utility of VFC in synthetic and biological data, and show how VFC can be used to identify observations with similar feature sets and signal profiles.

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Identification of druggable binding sites and small molecules as modulators of TMC1

Communications Biology

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Communications Biology 2025年第1期8卷 1-22页

作者： De-la-Torre, Pedro Martínez-García, Claudia Gratias, Paul Mun, Matthew Santana, Paula Akyuz, Nurunisa González, Wendy Indzhykulian, Artur A. Ramírez, David Department of Otolaryngology - Head and Neck Surgery Harvard Medical School and Mass Eye and Ear Boston MA United States Departamento de Farmacología Facultad de Ciencias Biológicas Universidad de Concepción Concepción Chile Speech and Hearing Bioscience & Technology Program Division of Medical Sciences Harvard University Boston MA United States Facultad de Ingeniería Instituto de Ciencias Aplicadas Universidad Autónoma de Chile Santiago Chile Department of Neurobiology Harvard Medical School Boston MA United States Center for Bioinformatics Simulations and Modelling (CBSM) University of Talca Talca Chile Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia Life Sciences Research Center Universidad Simón Bolívar Barranquilla Colombia

Our ability to hear and maintain balance relies on the proper functioning of inner ear sensory hair cells, which translate mechanical stimuli into electrical signals via mechano-electrical transducer (MET) channels, composed of TMC1/2 proteins. However, the therapeutic use of ototoxic drugs, such as aminoglycosides and cisplatin, which can enter hair cells through MET channels, often leads to profound auditory and vestibular dysfunction. To date, our understanding of how small-molecule modulators interact with TMCs remains limited, hampering the discovery of novel drugs. Here, we propose a structure-based drug screening approach, integrating 3D-pharmacophore modeling, molecular dynamics simulations of the TMC1 + CIB2 + TMIE complex, and experimental validation. Our pipeline successfully identified three potential drug-binding sites within the TMC1 pore, phospholipids, and key amino acids involved in the binding of several compounds, as well as FDA-approved drugs that reduced dye uptake in cultured cochlear explants. Our pipeline offers a broad application for discovering modulators for mechanosensitive ion channels. © The Author(s) 2025.

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Discovery Biological Motifs Using Heuristics Approaches

Discovery Biological Motifs Using Heuristics Approaches

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Brazilian Conference on Intelligent Systems (BRACIS)

作者： Jader M. Caldonazzo Garbelini André Yoshiaki Kashiwabara Danilo Sipoli Sanches Graduate Program in Bioinformatics (PPGBIOINFO) Federal University of Technology Cornélio Procópio PR Brazil

ISBN: (纸本)9781509035670

The identification of transcription factors binding sites (TFBS) - also called motifs - in DNA sequences is the first step to understanding how works gene regulation. Recognizing these patterns in the promoter regions of co-expressed genes is a determining key for this. Although there are several algorithms for this purpose, the problem is still far from being solved because of the great diversity of gene expression and the binding sites low specificity. State of the art algorithms have limitations, such as the high number of false positives and low accuracy for Identifying weak motifs. In this article we proposed a new approach based on memetic algorithms (DMMA) for discovery mofifs. The proposed approach was developed using evolutionary computation along with the local search algorithms simulated annealing and variable neighborhood search. To attest the algorithm ability, tests were conducted in four datasets - two real and two synthetic - and the results were compared with other approaches in the literature.

关键词： Sociology Statistics Complexity theory Biology Probability Mathematical model Simulated annealing

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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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Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development

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Developmental Cell 2025年

作者： Chakraborty, Shreeta Wenzlitschke, Nina Anderson, Matthew J. Eraso, Ariel Baudic, Manon Thompson, Joyce J. Evans, Alicia A. Shatford-Adams, Lilly M. Chari, Raj Awasthi, Parirokh Dale, Ryan K. Lewandoski, Mark Petros, Timothy J. Rocha, Pedro P. Unit on Genome Structure and Regulation National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Genetics of Vertebrate Development Section Cancer and Developmental Biology Laboratory National Cancer Institute National Institutes of Health Frederick 21702 MD United States Bioinformatics and Scientific Programming Core National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States Laboratory Animal Sciences Program Frederick National Laboratory for Cancer Research Frederick 21702 MD United States Unit on Cellular and Molecular Neurodevelopment National Institute of Child Health and Human Development National Institutes of Health Bethesda 20892 MD United States National Cancer Institute NIH Bethesda 20892 MD United States

Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysregulation and phenotypes. We tested whether perturbing a domain with multiple developmental regulators would lead to more severe outcomes. We chose a domain with three FGF ligand genes—Fgf3, Fgf4, and Fgf15—that control different murine developmental processes. Heterozygous deletion of a 23.9-kb boundary defined by four CTCF sites led to ectopic interactions of the FGF genes with enhancers active in the brain and induced FGF expression. This caused orofacial clefts, encephalocele, and fully penetrant perinatal lethality. Loss of the single CTCF motif oriented toward the enhancers—but not the three toward the FGF genes—recapitulated these phenotypes. Our works shows that small sequence variants at particular domain boundaries can have a surprisingly outsized effect and must be considered as potential sources of gene dysregulation in development and disease. © 2025

关键词： CTCF epigenetics FGF gene regulation nuclear organization

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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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An obstetric brachial plexus lesion rehabilitation platform

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Research on Biomedical Engineering 2019年第2期35卷 167-172页

作者： Alberti, Eduardo Juliano Pichorim, Sérgio Francisco Brawerman, Alessandro Curitiba Paraná80230-901 Brazil Computer Engineering School Coordenação de Engenharia da Computação Positivo University Bloco Vermelho Sala 217 Rua Professor Pedro Viriato Parigot de Souza 5300 – Campo Comprido CuritibaParaná Brazil Bioinformatics Graduate Program Federal University of Paraná CuritibaParaná Brazil

Purpose: Obstetric brachial plexus lesions (OBPL) are caused by the lesion or rupture of the cervical and thoracic nerves during birth. Physical therapy, based on ludic activities, can be useful to improve the OBPL treatment in children. This paper proposes a rehabilitation platform with a ludic interface (lights and sounds), using the magnitude motion gain of a user to aid in the OBPL treatment. Methods: The motor development table (MDT) is an electronic platform composed of eight light segments (with green and red LEDs) that detect the touch of a child’s hand (by optic proximity sensors). Each touch generates a different sound, depending on the exercise. The physiotherapist can choose the MDT game, and the child score can be recorded. The operation of the rehabilitation platform was tested in relation to its behavior depending on the environmental lighting, its efficiency in data processing, and its maximum distance of drive. We also applied an opinion survey. Results: The tests showed that the MDT can be used in environments with up to 1015 lx of illumination and that the incidence of high-intensity light affects the segments’ ability to detect the hand. In addition, the tests demonstrated that the behavior of this device is not affected by the number of errors or triggers performed during the exercises. Conclusion: Based on these findings and on the opinion survey, it is possible to conclude that the MDT can reliably assist the physiotherapist in orthopedic management by providing feedback from the sessions and the patients’ temporal progress. © 2019, Sociedade Brasileira de Engenharia Biomedica.

关键词： Digital storage

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Expression of Gli1 in the hedgehog signaling pathway and breast cancer recurrence

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Chinese Journal of Cancer Research 2012年第4期24卷 257-258页

作者： Naoko Takebe Sally Hunsberger Sherry X.Yang Cancer Therapy Evaluation Program Bioinformatics Research Branch National Clinical Target Validation Laboratory Division of Cancer Treatment and DiagnosisNational Cancer InstituteNational Institutes of HealthUSA

The hedgehog （Hh） signaling pathway plays an essential role in the embryonic development and homeostasis of diverse adult tissues, and its deregulation has been implicated in the tumorigenesis and metastasis of various malignancies including breast cancer. Aberrant activation of the Hh pathway includes the following mechanisms：（I） Hh ligand-independent mechanism - Loss of function mutations in the Hh receptor Patched 1 （PTCH1） or gain of function mutations in the Smoothened （SMO） lead to constitutive activation of this pathway; （II） Autocrine signaling- Ith ligand produced by tumor cells stimulates the Hh signaling in tumor cells; （III） Paracrine signaling - tumor cell produced-Hh ligand activates stromal and endothelial cells that produce growth factors in microenvironment for supporting tumor growth and survival; and （IV） Reverse paracrine signaling - Hh ligand produced by stromal cells support tumor growth and survival. Upon the pathway activation, the Gli transcription factors, effectors of the Hh signaling, activate or inhibit transcription by binding to their responsive genes and interacting with the transcriptional complex. The Gli transcription factor family includes Glil, Gli2, and Gli3 （1）. Glil is a transcriptional activator whose expression has been recognized as an activation state of the Hh signaling pathway, Gli2 is either an activator or repressor, and Gli3 is a strong repressor of transcriptional activities. To date, a ligand-dependent autocrine model of activating the Hh signaling has been described in breast cancer, and both an autocrine and paracrine mechanisms in colorectal cancer, pancreatic cancer and prostate cancer （2,3）. Notably, a ligand-independent mechanism （mutationsin PTCHI and SMO） of the signaling has been well demonstrated in basal cell carcinoma and medulloblastoma （4,5）.

关键词： cell Expression of Gli1 in the hedgehog signaling pathway and breast cancer recurrence

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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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Using a Recurrent Neural Network Model for Classification of Tweets Conveyed Influenza-related Information 1

Using a Recurrent Neural Network Model for Classification of...

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1st International Workshop on Digital Disease Detection using Social Media, DDDSM 2017, co-located with the 8th International Joint Conference on Natural Language Processing, IJCNLP 2017

作者： Wang, Chen-Kai Singh, Onkar Tang, Zhao-Li Dai, Hong-Jie Graduate Institute of Biomedical Informatics Taipei Medical University Taipei Taiwan Bioinformatics Program Taiwan International Graduate Program Institute of Information Science Academia Sinica Taipei Taiwan Institute of Biomedical Informatics National Yang-Ming University Taipei Taiwan Department of Computer Science and Information Engineering National Taitung University Taitung Taiwan Interdisciplinary Program of Green and Information Technology National Taitung University Taitung Taiwan

ISBN: (纸本)9781948087070

Traditional disease surveillance systems depend on outpatient reporting and virological test results released by hospitals. These data have valid and accurate information about emerging outbreaks but it's often not timely. In recent years the exponential growth of users getting connected to social media provides immense knowledge about epidemics by sharing related information. Social media can now flag more immediate concerns related to outbreaks in real time. In this paper we apply the long short-term memory recurrent neural network (RNN) architecture to classify tweets conveyed influenza-related information and compare its performance with baseline algorithms including support vector machine (SVM), decision tree, naive Bayes, simple logistics, and naive Bayes multinomial. The developed RNN model achieved an F-score of 0.845 on the MedWeb task test set, which outperforms the F-score of SVM without applying the synthetic minority oversampling technique by 0.08. The F-score of the RNN model is within 1% of the highest score achieved by SVM with oversampling technique. © 2017 AFNLP

关键词： Support vector machines

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