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Context-dependent gene regulatory network reveals regulation dynamics and cell trajectories using unspliced transcripts

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Briefings in bioinformatics 2023年第2期24卷 bbac633-bbac633页

作者： Tu, Yueh-Hua Juan, Hsueh-Fen Huang, Hsuan-Cheng The Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taiwan Department of Life Science Center for Computational and Systems Biology National Taiwan University Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taiwan

Gene regulatory networks govern complex gene expression programs in various biological phenomena, including embryonic development, cell fate decisions and oncogenesis. Single-cell techniques are increasingly being used to study gene expression, providing higher resolution than traditional approaches. However, inferring a comprehensive gene regulatory network across different cell types remains a challenge. Here, we propose to construct context-dependent gene regulatory networks (CDGRNs) from single-cell RNA sequencing data utilizing both spliced and unspliced transcript expression levels. A gene regulatory network is decomposed into subnetworks corresponding to different transcriptomic contexts. Each subnetwork comprises the consensus active regulation pairs of transcription factors and their target genes shared by a group of cells, inferred by a Gaussian mixture model. We find that the union of gene regulation pairs in all contexts is sufficient to reconstruct differentiation trajectories. Functions specific to the cell cycle, cell differentiation or tissue-specific functions are enriched throughout the developmental process in each context. Surprisingly, we also observe that the network entropy of CDGRNs decreases along differentiation trajectories, indicating directionality in differentiation. Overall, CDGRN allows us to establish the connection between gene regulation at the molecular level and cell differentiation at the macroscopic level. © The Author(s) 2023.

关键词： Gaussian mixture model gene regulatory network single-cell RNA sequencing trajectory analysis

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Predicting drug response through tumor deconvolution by cancer cell lines

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Patterns 2024年第4期5卷 100949页

作者： Hsu, Yu-Ching Chiu, Yu-Chiao Lu, Tzu-Pin Hsiao, Tzu-Hung Chen, Yidong Bioinformatics Program Taiwan International Graduate Program National Taiwan University Taipei115 Taiwan Bioinformatics Program Institute of Statistical Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Health Data Analytics and Statistics Department of Public Health College of Public Health National Taiwan University Taipei100 Taiwan Greehey Children's Cancer Research Institute University of Texas Health San Antonio San AntonioTX78229 United States Department of Medicine School of Medicine University of Pittsburgh PittsburghPA15261 United States UPMC Hillman Cancer Center University of Pittsburgh PittsburghPA15232 United States Department of Medical Research Taichung Veterans General Hospital Taichung40705 Taiwan Department of Population Health Sciences University of Texas Health San Antonio San AntonioTX78229 United States

Large-scale cancer drug sensitivity data have become available for a collection of cancer cell lines, but only limited drug response data from patients are available. Bridging the gap in pharmacogenomics knowledge between in vitro and in vivo datasets remains challenging. In this study, we trained a deep learning model, Scaden-CA, for deconvoluting tumor data into proportions of cancer-type-specific cell lines. Then, we developed a drug response prediction method using the deconvoluted proportions and the drug sensitivity data from cell lines. The Scaden-CA model showed excellent performance in terms of concordance correlation coefficients (>0.9 for model testing) and the correctly deconvoluted rate (>70% across most cancers) for model validation using Cancer Cell Line Encyclopedia (CCLE) bulk RNA data. We applied the model to tumors in The Cancer Genome Atlas (TCGA) dataset and examined associations between predicted cell viability and mutation status or gene expression levels to understand underlying mechanisms of potential value for drug repurposing. © 2024 The Authors

关键词： Tumors

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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A Hydrodynamic Analysis of Water System in Dadahup Swamp Irrigation Area 1

A Hydrodynamic Analysis of Water System in Dadahup Swamp Irr...

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1st International Conference on Computer Science and Artificial Intelligence, ICCSAI 2021

作者： Purboseno, Sentot Suparyanto, Teddy Hidayat, Alam Ahmad Pardamean, Bens Institute of Agriculture STIPER Department of Agricultural Engineering Yogyakarta55283 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center BINUS Graduate Program-Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781728133331

Dadahup Swamp Irrigation Area (DIR) in Kapuas Regency, Central Kalimantan is developed for agricultural activities to provide food security after the pandemic. The water system consists of various channels, gates, and a flood embankment structure, which is also connected to three different rivers: Barito River, Mangkatif River, and Kapuas Mumpung River. To quantify flood risk assessments in the area, we perform a hydrodynamic analysis using the unsteady flow method via HEC-RAS software version 4.1.0. We use geometrical profiles from topography measurements and the outer boundary of the Dadahup DIR as input for the hydrologic model. Our results estimate the maximum surface water level from both cross and longitudinal sections in the channels and find that several points near the flood embankment area are prone to flood events. Our modeling approach provides a preliminary assessment for the local government to formulate a flood mitigation plan and policy in the area. © 2021 IEEE.

关键词： Rivers

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Automatic Multiple Choice Question Generation: A Systematic Literature Review

Automatic Multiple Choice Question Generation: A Systematic ...

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Information Technology and Digital Applications (ICITDA), IEEE International Conference on

作者： Matthew Martianus Henry Nur Adhianti Heryanto Mahmud Isnan Kuncahyo Setyo Nugroho Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331510732

ISBN: (纸本)9798331510749

Despite their drawbacks, multiple-choice questions (MCQ) have been widely used to assess the students' understanding of lectures through examinations. The development of automatic MCQ generation is beneficial, especially for educators. As a starting point for further development, a Systematic Literature Review (SLR) is conducted to uncover current trends, future challenges, and opportunities in automatic MCQ generation. Previously, an SLR was conducted, but it lacks coverage of the utilization of transformer-based models. This SLR covers the development of automatic MCQ generation using either traditional or advanced approaches such as Transformers. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses framework was used to gather the data from Scopus, IEEE Xplore, SpringerLink, arXiv, and Semantic Scholar. The included articles must be open-access computer science conference papers or journal articles and written in English less than five years ago. Four independent reviewers analyzed the research workflow, evaluation metric, and dataset used in each study. There are 18 included studies, where 17% (n = 3) studies are from 2024, 33% (n = 6) studies are from 2023, 22% (n = 4) studies are from 2022, 11% (n = 2) studies are from 2021, and 17% (n = 3) studies are from 2020. There are 33% (n = 6) of the studies used the traditional feature-based engineering approach, 39% (n = 7) of the studies used the Transformer-based model fine-tuning approach, and the remaining used novel approaches. The study found that BERT variants are the most utilized Transformer-based model in automatic MCQ. The research notes some challenges, but also open various opportunities for further research, including Large Language Model (LLM) utilization for automatic MCQ generation, the utilization BERT-based models for standardized machine-learned evaluation metrics, and the initiative for the creation of an MCQ dataset benchmark.

关键词： Measurement Semantics Reinforcement learning Benchmark testing Ontologies Transformers Question generation Prompt engineering Standards Systematic literature review

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Comparative Analysis of CNN Models for Multiclass Detection on Colon Disease

Comparative Analysis of CNN Models for Multiclass Detection ...

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Information Technology and Digital Applications (ICITDA), IEEE International Conference on

作者： Jason Sebastian Sulistyawan Kuncahyo Setyo Nugroho Mahmud Isnan Bens Pardamean Computer Science Department BINUS Graduate Program - Master of Computer Science Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta Indonesia

ISBN: (数字)9798331510732

ISBN: (纸本)9798331510749

Gastrointestinal diseases are significant health concerns that mostly affect the digestive and biliary tracts. These can only be observed internally through endoscopy, or a modern approach named Wireless Capsule Endoscopy. Though the approach has proven to work, the process relies heavily on medical experts, which is prone to error when given a considerably large load. The use of deep learning in detecting diseases with images has been proven to work in various cases and can be implemented for gastrointestinal diseases. This study compared four deep learning models based on Convolutional Neural Network architectures consisting of the VGG16, ResNet152V2, InceptionV3, and Xception for classifying colon disease images. The experiment showed that the ResNet152V2 performed the best, compared to the other three with a testing accuracy score of 0.9837. On the other hand, the VGG16 had the lowest performance with around accuracy score of 0.89 while the Xception and InceptionV3models yielded similar accuracy scores of 0.9587 and 0.9549, respectively. The results highlight the effectiveness of ResNet152V2 in handling the complexity of colon disease detection

关键词： Hands Deep learning Accuracy Endoscopes Real-time systems Gastrointestinal tract Data models Colon Medical diagnostic imaging Diseases

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A bioinformatics Analysis and Homology 3D Modeling of Dihydroxy-orotate-dehydrogenase of Plasmodium ovale

A Bioinformatics Analysis and Homology 3D Modeling of Dihydr...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Rudi Nirwantono Khoirunnisa Assidqi Alam Ahmad Hidayat Joko Pebrianto Trinugroho Bens Pardamean Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Food Biotechnology Research Center Bina Nusantara University Jakarta Indonesia Mathematics Departement School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta Indonesia

The infection of Plasmodium vivax is relatively less virulent than the deathliest Plasmodium falciparum. However, it still can lead to a fatal case and often induces recurring malaria due to dormant parasites in the liver. Thus, the research to study the drug to treat Plasmodium vivax is essential, where the enzyme dihydroorotate dehydrogenase (DHODH) has recently become a new drug target. However, the drug-enzyme interaction study has only recently been conducted in Plasmodium falciparum (pfDHODH) due to the lack of the 3D structure of enzyme DHODH from Plasmodium vivax that is crucial for the study. Therefore, this study aimed to perform the modelling study of Plasmodium vivax DHODH (PvDHODH) to create a 3D structure as a basis for drug-protein interaction study in upcoming studies. Sequence pvDHODH (Accession: SCO68359.1) was used in homology modelling using Modeller 10.2 with the crystal structure of DHODH from DHODH (Accession: 7KZY) as a template. Overall, the model generated from the homology modelling was considered a good model, and the 3D structure was close to the native state according to several parameters, including DOPE score, GA341 score, QMEAN4 value, 3D-1D score, ERRAT2 score, and ProSA score. Ramachandran plot also revealed that almost all amino acids were distributed in the desirable and allowed area (99.1%), and only 0.9% were in generously allowed regions. Superimposition of the model with the template also indicated that the model has an almost similar structure and amino acids positioning, including in the binding pocket and active site. Therefore, the model can be used for downstream analysis in drug-protein interaction studies. Nevertheless, some improvements can still be performed to upgrade the quality of the model by deleting unaligned residues on the C-terminal and realigning the residues at the doubting site.

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Systematic Literature Review on Statistics and Machine Learning Predictive Models for Rice Phenotypes

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Procedia Computer Science 2023年 227卷 1054-1061页

作者： Nicholas Dominic Tjeng Wawan Cenggoro Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta 11480 Indonesia

Predicting the best-quality of rice phenotypes is the priority among agricultural researchers to fulfill worldwide food security. Trend development of predictive models from statistics to machine learning is the subject of this review. Gathered from the Google Scholar database, 14 appropriate papers (2016-2020) related to the rice phenotypes prediction were selected through title and abstract content filtering. The outputs show that Support Vector Machine, Multi-layer Perceptron, and regression are the most used models, while yield is the priority prediction point besides tiller, panicle, and 1000-grain weight of rice. However, finding the accurate predictor is invariably challenging due to distinct rice varieties in the world and high confounding factors. Thus, developing an advanced deep learning model that accommodates these needs is worth considering further.

关键词： rice phenotypes prediction statistics machine learning

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Web Development of Direct-to-consumer Genetics Testing 4

Web Development of Direct-to-consumer Genetics Testing

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4th International Conference on Cybernetics and Intelligent System, ICORIS 2022

作者： Azizatikarna, Kians Parung, Deby Erina Amirullah, Dian Hidayat, Alam Ahmad Cenggoro, Tjeng Wawan Budiarto, Arif Simon Pardamean, Bens Genetics Indonesia Jakarta12940 Indonesia Bina Nusantara University Bioinformatics and Data Science Research Center Jakarta11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta11480 Indonesia Bina Nusantara University BINUS Graduate Program - Master of Computer Science Computer Science Department Jakarta11480 Indonesia

ISBN: (纸本)9781665453950

As the cost of genetic testing becomes more affordable each year, direct-to-customer (DTC) genetic testing services witness rapid market growth. This has encouraged the development of an easy-to-use website application to optimize potential customers to obtain informed choice regarding the offered DTC genetic testing as well as purchasing information. We present a wireframing process as a part of the agile software development process to build a web portal prototype for an Indonesia-based genetic testing service called DNAku. The approach in building the prototype used in this case is a part of the Agile Software Development Method. In brief, the wireframing stage resulted in this work consists of three main important outcomes. The first one is the use case diagram as a blueprint of this web-based system. A site map is then proposed as an extended version of the use case diagram which visualizes the whole pages with the links. Finally, based on this site map a series of page mock-ups are designed using Hyper Text Marking Language (HTML) and Cascading Style Sheets (CSS). The result of the prototype can be used as the basis for the next development stage, which is the coding stage based on the collected feedback from users. Considering the continuous application development via the wireframing method by taking into account the cycle of feedbacks from involved parties, this approach can strengthen the infrastructure to sustain DTC genetic business model, which has a niche market in Indonesia. © 2022 IEEE.

关键词： Sales

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Characterization of Antioxidative Flavonoids in Wild and Cultivated Soybean by Ion-Filtering Strategy-Combined Lc-Hrmsn Analysis

SSRN

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SSRN 2024年

作者： No, Kyoung Tai Kim, Kwan Joong Cho, Min Hyung Lee, Sangwon Ha, Jang-Ho Chu, Sung-June Chung, Gyuhwa Kim, Dae-Ok Bioinformatics & Molecular Design Research Center Incheon21983 Korea Republic of Department of Biotechnology Chonnam National University Yeosu59626 Korea Republic of Graduate School of Biotechnology Kyung Hee University Yongin17104 Korea Republic of Interdisciplinary Graduate Program Department of Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of Yonsei University Korea Republic of

To profiling flavonoids in wild soybean (WB;Glycine soja Sieb & Zucc.) and cultivated soybean (CB;Glycine max (L.) Merr.), liquid chromatography-high resolution mass spectrometry (LC-HRMS), antioxidant assays, and chemometrics method were used. Total 70 flavonoids were tentatively identified with ion filter strategies containing precursor ion list, mass defect filter, nitrogen rule filter, and diagnostic ion filter from 20,999 features in WB and CB. Semi-quantification result revealed that WB has 1.4-, 93.1-, 6.3-, and 1.9-fold higher contents in isoflavone, flavan, procyanidin, and flavone than that of CB. In antioxidant assays, WB showed 1.89- to 5.83-fold higher antioxidant capacities than CB in four antioxidant capacity assays. In orthogonal partial least squares discriminant analysis, WB and CB were clearly classified, and 31 characteristic flavonoids were identified by variable importance in projection. Furthermore, epicatechin and procyanidins of WB showed significantly positive correlation with antioxidant capacities by Pearson's correlation. © 2024, The Authors. All rights reserved.

关键词： Flavonoids

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