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SeqCP: A sequence-based algorithm for searching circularly permuted proteins

Computational and Structural Biotechnology Journal 2023年 21卷 185-201页

作者： Chen, Chi-Chun Huang, Yu-Wei Huang, Hsuan-Cheng Lo, Wei-Cheng Lyu, Ping-Chiang Bioinformatics Program Institute of Information Science Taiwan International Graduate Program Academia Sinica Taipei115 Taiwan Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300 Taiwan Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu300 Taiwan Institute of Biomedical Informatics National Yang Ming Chiao Tung University Taipei112 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu300 Taiwan The Center for Bioinformatics Research National Yang Ming Chiao Tung University Hsinchu Taiwan

Circular permutation (CP) is a protein sequence rearrangement in which the amino- and carboxyl-termini of a protein can be created in different positions along the imaginary circularized sequence. Circularly permutated proteins usually exhibit conserved three-dimensional structures and functions. By comparing the structures of circular permutants (CPMs), protein research and bioengineering applications can be approached in ways that are difficult to achieve by traditional mutagenesis. Most current CP detection algorithms depend on structural information. Because there is a vast number of proteins with unknown structures, many CP pairs may remain unidentified. An efficient sequence-based CP detector will help identify more CP pairs and advance many protein studies. For instance, some hypothetical proteins may have CPMs with known functions and structures that are informative for functional annotation, but existing structure-based CP search methods cannot be applied when those hypothetical proteins lack structural information. Despite the considerable potential for applications, sequence-based CP search methods have not been well developed. We present a sequence-based method, SeqCP, which analyzes normal and duplicated sequence alignments to identify CPMs and determine candidate CP sites for proteins. SeqCP was trained by data obtained from the Circular Permutation Database and tested with nonredundant datasets from the Protein Data Bank. It shows high reliability in CP identification and achieves an AUC of 0.9. SeqCP has been implemented into a web server available at: http://***/SeqCP/. © 2022 The Authors

关键词： Proteins

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Multi-objective design of synthetic biological circuits

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IFAC-PapersOnLine 2017年第1期50卷 9871-9876页

作者： Lormeau C. Rybiński M. Stelling J. Department of Biosystems Science and Engineering ETH Zurich SIB Swiss Institute of Bioinformatics Life Science Zurich Ph.D. program ”Systems Biology” Basel 4058 Switzerland Department of Biosystems Science and Engineering ETH Zurich SIB Swiss Institute of Bioinformatics Basel 4058 Switzerland

Computational methods enable the design of synthetic biological circuits demonstrating a specific dynamic behavior. Current methods are based on the assembly of parts characterized in different contexts, which often fail to operate as predicted when combined. Here we introduce a circuit design method that compensates for parts uncertainty by identifying circuit topologies whose behavior is robust to variations in parameters. Our heuristic topological filtering approach efficiently yields robust circuit designs in a Bayesian framework, and enables to reliably assess trade-offs between performance, robustness, and experimental feasibility, thus increasing the probability of success of circuit implementation. © 2017

关键词： Biocybernetics Computer-aided circuit design Multiobjective optimisations Robustness Synthetic biology

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Investigation of RNA-RNA Interactions Using the RISE Database

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Current Protocols in bioinformatics 2018年第1期64卷 e58/1-e58/1页

作者： Ju, Yanyan Gong, Jing Yang, Yucheng T. Zhang, Qiangfeng Cliff MOE Key Laboratory of Bioinformatics Beijing Advanced Innovation Center for Structural Biology Center for Synthetic and Systems Biology Tsinghua-Peking Joint Center for Life Sciences School of Life Sciences Tsinghua University Beijing China Department of Molecular Biophysics and Biochemistry Yale University New Haven CT United States Program in Computational Biology and Bioinformatics Yale University New Haven CT United States

RNA-RNA interactions (RRIs) are essential to understanding the regulatory mechanisms of RNAs. Mapping RRIs in vivo in a transcriptome-wide manner remained challenging until the recent development of several sequencing-based technologies. However, RRIs generated from large-scale studies had not been systematically collected and analyzed before. This article introduces RISE, a database of the RNA Interactome from Sequencing Experiments. RISE provides a comprehensive collection of RRIs in human, mouse, and yeast, derived from transcriptome-wide sequencing experiments, as well as targeted sequencing studies and other public databases/datasets. To facilitate better understanding of the biological roles of these RRIs, RISE also offers rich functional annotations involving RNAs, and an interactive interface to explore the analysis results. Here, we provide a brief description of the RISE website and a step-by-step protocol for using RISE to study RRIs. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

关键词： interaction RISE RNA RNA structure RNA-RNA sequencing experiments

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Innovative computational advances for disease outbreaks

Innovative computational advances for disease outbreaks

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World Congress on Engineering 2016, WCE 2016

作者： Gebreyesus, Kidane Desta Chang, Chuan-Hsiung Institute of Information Science Bioinformatics Program Taiwan International Graduate Program Academia Sinica Taipei 115 Taiwan Center for Systems and Synthetic Biology Institute of Biomedical Informatics National Yang-Ming University Taipei 112 Taiwan

ISBN: (纸本)9789881925305

SIR (susceptible, infectious, removed) epidemic models are commonly used in infectious disease study. These models use systems of differential equations to estimate epidemiological parameters. However, differential equations often suffer from numerical challenges. Here, we proposed simple, effective and robust innovative methods for estimating key infectious disease parameters. Our methods are reformed from the SIR models, by adjusting components of model compartments. We illustrated the methods using the recent large disease outbreaks, Ebola virus disease and Middle East respiratory syndrome Coronavirus.

关键词： Coronavirus

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miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament 4

miRNA networks regulating gene expression in response to ten...

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4th IEEE International Conference on BioInspired Processing, BIP 2022

作者： Valverde, Mariana Bonilla Rodriguez, Rodrigo Mora University of Costa Rica Postgraduate Program Sep Master Program on Bioinformatics and Systems Biology San José11501-2060 Costa Rica University of Costa Rica Faculty of Microbiology San José11501-2060 Costa Rica

ISBN: (纸本)9781665470483

In response to force application, biological reactions occur in the periodontal ligament that causes the orthodontic tooth movement. Differential expression of genes such as ALPL, FGF7, PDRM1, and NR4A2 are involved in the exposure to tension or compression forces by contributing to bone remodeling. In this study, a systems biology approach is used in order to identify a modulator of gene expression when mechanical loadings are applied in periodontal ligament cells. We developed a mathematical model of the interaction network of ALPL and FGF7 with several miRNAs and the transcription factor modulators in BioNetUCR, Cytoscape and COPASI software. We found that miR129-2 has a negative control in ALPL, FGF7, NR4A2 and PRDM1 genes, while miRNA192 has a negative control in ALPL and FGF7 genes in compression and tension side. Both miRNAs are proposed for future experimental validation. © 2022 IEEE.

关键词： RNA

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Peak analysis of cell-free RNA finds recurrently protected narrow regions with clinical potential

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Genome biology 2025年第1期26.0卷 1-25页

作者： Bao, Pengfei Wang, Taiwei Liu, Xiaofan Xing, Shaozhen Ruan, Hanjin Ma, Hongli Tao, Yuhuan Zhan, Qing Belmonte-Reche, Efres Qin, Lizheng Han, Zhengxue Mao, Minghui Li, Mengtao Lu, Zhi John MOE Key Laboratory of Bioinformatics State Key Lab of Green Biomanufacturing Center for Synthetic and Systems Biology School of Life Sciences Tsinghua University Beijing 100084 China Institute for Precision Medicine Tsinghua University Beijing 100084 China Peking University–Tsinghua University–National Institute of Biological Sciences Joint Graduate Program School of Life Sciences Tsinghua University Beijing China Department of Rheumatology and Clinical Immunology Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100730 China National Clinical Research Center for Dermatologic and Immunologic Diseases (Ministry of Science & Technology) MOE Key Laboratory of Rheumatology and Clinical Immunology State Key Laboratory of Complex Severe and Rare Diseases Peking Union Medical College Hospital Beijing 100730 China Academy for Advanced Interdisciplinary Studies (AAIS)and Sciences Joint Graduate Program (PTN) Peking University Beijing China Department of Oral and Maxillofacial & Head and Neck Oncology Beijing Stomatological Hospital Capital Medical University Beijing China Centre for Genomics and Oncological Research (GENYO) Avenida de La Ilustración 114 Granada 18016 Spain Department of Biochemistry and Molecular Biology II Faculty of Pharmacy University of Granada Granada Spain Instituto de Investigación Biosanitaria Ibs.GRANADA Hospital Virgen de Las Nieves Granada Spain The Center for Regeneration Aging and Chronic Diseases School of Basic Medical Sciences Tsinghua University Beijing China

Background: Cell-free RNAs (cfRNAs) can be detected in biofluids and have emerged as valuable disease biomarkers. Accurate identification of the fragmented cfRNA signals, especially those originating from pathological cells, is crucial for understanding their biological functions and clinical value. However, many challenges still need to be addressed for their application, including developing specific analysis methods and translating cfRNA fragments with biological support into clinical applications. Results: We present cfPeak, a novel method combining statistics and machine learning models to detect the fragmented cfRNA signals effectively. When test in real and artificial cfRNA sequencing (cfRNA-seq) data, cfPeak shows an improved performance compared with other applicable methods. We reveal that narrow cfRNA peaks preferentially overlap with protein binding sites, vesicle-sorting sites, structural sites, and novel small non-coding RNAs (sncRNAs). When applied in clinical cohorts, cfPeak identified cfRNA peaks in patients’ plasma that enable cancer detection and are informative of cancer types and metastasis. Conclusions: Our study fills the gap in the current small cfRNA-seq analysis at fragment-scale and builds a bridge to the scientific discovery in cfRNA fragmentomics. We demonstrate the significance of finding low abundant tissue-derived signals in small cfRNA and prove the feasibility for application in liquid biopsy. © The Author(s) 2025.

关键词： Cell-free RNA CfRNA fragment Liquid biopsy biomarker Noninvasive cancer detection Peak calling SncRNA Tissue-of-origin

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Statistical measures on residue-level protein structural properties

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Journal of Structural and Functional Genomics 2011年第2期12卷 119-136页

作者： Huang, Yuanyuan Bonett, Stephen Kloczkowski, Andrzej Jernigan, Robert Wu, Zhijun Program on Bioinformatics and Computational Biology Iowa State University Ames IA 50014 United States Summer REU Program on Computational Systems Biology Iowa State University Ames IA 50014 United States Department of Biochemistry Biophysics and Molecular Biology Iowa State University Ames IA 50014 United States Department of Mathematics Iowa State University Ames IA 50014 United States

The atomic-level structural properties of proteins, such as bond lengths, bond angles, and torsion angles, have been well studied and understood based on either chemistry knowledge or statistical analysis. Similar properties on the residue-level, such as the distances between two residues and the angles formed by short sequences of residues, can be equally important for structural analysis and modeling, but these have not been examined and documented on a similar scale. While these properties are difficult to measure experimentally, they can be statistically estimated in meaningful ways based on their distributions in known proteins structures. Residue-level structural properties including various types of residue distances and angles are estimated statistically. A software package is built to provide direct access to the statistical data for the properties including some important correlations not previously investigated. The distributions of residue distances and angles may vary with varying sequences, but in most cases, are concentrated in some high probability ranges, corresponding to their frequent occurrences in either α-helices or β-sheets. Strong correlations among neighboring residue angles, similar to those between neighboring torsion angles at the atomic-level, are revealed based on their statistical measures. Residue-level statistical potentials can be defined using the statistical distributions and correlations of the residue distances and angles. Ramachandran-like plots for strongly correlated residue angles are plotted and analyzed. Their applications to structural evaluation and refinement are demonstrated. With the increase in both number and quality of known protein structures, many structural properties can be derived from sets of protein structures by statistical analysis and data mining, and these can even be used as a supplement to the experimental data for structure determinations. Indeed, the statistical measures on various types of residue d

关键词： Protein structural analysis Residue-level structural properties Statistical methods Statistical potentials Structural bioinformatics Structural correlation plots Structural databases

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A Model of Amylopectin Biosynthesis based on the Activities of Key Enzymes Coupled with the Crystallization Process

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Procedia Computer Science 2013年 23卷 53-59页

作者： Teeraphan Laomettachit Bioinformatics and Systems Biology Program School of Bioresources and Technology King Mongkut's University of Technology Thonburi Bangkok 10140 Thailand

Amylopectin is the major glucose polymer in the plant starch granule. The amylopectin molecules have a highly ordered structure of alternating regions between the crystalline and amorphous lamellae, which is distinct from glycogen (the principle form of carbohydrate storage in bacteria and animals). Although several key enzymes involved in the amylopectin biosynthesis have been studied extensively, the underlying mechanism that gives rise to the unique structure of amylopectin remains largely unknown. In the present work, the Monte Carlo simulation technique is used to study the roles of the key enzymes and their relationship in the biosynthesis of amylopectin. We propose a mechanism of the amylopectin biosynthesis based on the activities of the key enzymes coupled with the crystallization process. The proposed mechanism can explain the characteristics of the molecular weight distributions of the molecules and how the amylopectin structure arises.

关键词： amylopectin starch biosynthesis Monte Carlo simulation

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Reliable protocols for whole-mount fluorescent in situ hybridization （FISH） in the pea aphid Acyrthosiphon pisum： A comprehensive survey and analysis

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Insect Science 2014年第3期21卷 265-277页

作者： Chen-yo Chung Charles E. Cook Gee-way Lin Ting-Yu Huang Chun-che Chang Laboratory for Genetics and Development Department ofEntomologyllnstitute of Biotechnology College ofBioresources andAgriculture National Taiwan University Taipei Taiwan European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge UK Research Center for Developmental Biology and Regenerative Medicine National Taiwan University Taipei Taiwan Institute of Biochemical Sciences College of Life Science National Taiwan University Taipei Taiwan Genome and Systems Biology Degree Program National Taiwan University Taipei Taiwan China

RNA in situ hybridization （ISH）, including chromogenic ISH （CISH） and fluorescent ISH （FISH）, has become a powerful tool for revealing the spatial distribution ofgene transcripts in model organisms. Previously, we developed a robust protocol for wholemount RNA CISH in the pea aphid Acyrthosiphon pisum, an emerging insect genomicmodel. In order to improve the resolving capacity of gene detection, we comprehensively surveyed current protocols of whole-mount RNA-FISH and developed protocols that allow,using confocal microscopy, clearer visualization of target messenger RNAs （mRNAs） - including those subcellularly localized and those with spatially overlapping expression. Wefind that Fast dye-based substrate fluorescence （SF）, tyramide signal amplification （TSA）, and TSA Plus all enable identifying gene expression thanks to multiplex amplificationof fluorescent signals. By contrast, methods of direct fluorescence （DF） do not allow visualizing signals. Detection of a single gene target was achieved with SF and TSA Plusfor most mRNAs, whereas TSA only allowed visualization of abundant transcripts such as Apvasl andAppiwi2 in the germ cells. For detection of multiple gene targets using doubleFISH, we recommend：（i） TSA/TSA, rather than TSA Plus/TSA Plus for colocalized mRNAs abundantly expressed in germ ceils, as proteinase K treatment can be omitted;and （ii） SF/TSA Plus for other gene targets such as Apenl and Apen2 as inactivation of enzyme conjugates is not required. SF/SF is not ideal for double FISH experiments due tosignal blurring. Based on these new conditions for RNA-FISH, we have obtained a better understanding of germline specification and embryonic segmentation in the pea *** anticipate that the RNA-FISH protocols for the pea aphid may also be used for other aphids and possibly other insect species, thus expanding the range of species from whichuseful insights into development and evolution may be obtained.

关键词： aphid fluorescence gene expression in situ hybridization model organism probe detection

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Special issue on RNA processing and regulation

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Frontiers of Electrical and Electronic Engineering in China 2018年第3期6卷 193-194页

作者： Xinshu Xiao Chaolin Zhang Department of Integrative Biology and Physiology Bioinformatics Interdepartmental ProgramMolecular Biology InstituteUniversity of California Los AngelesLos AngelesCA 90095USA Department of Systems Biology Department of Biochemistry and Molecular BiophysicsCenter for Motor Neuron Biology and DiseaseColumbia UniversityNew YorkNY 10032USA

This year （2018） marks the 60th anniversary of the ＂central dogma＂, summarized as ＂DNA makes RNA makes protein＂, which was originally proposed by Francis Crick in 1958. Three years later, messenger RNA was identified as the template of protein synthesis. After 60 years of discovery, including discovery of the split nature of eukaryotic genes （Le., splicing）, it becomes evident that messenger RNAs are not merely messengers, but a hub of co- and post-transcriptional regulation, which is fundamental to amplify the complexity encoded in the genome of higher eukaryotic organisms. The mature forms of RNA of protein-coding genes and their abundance have to be tightly regulated through multiple steps of sophisticated processing, including capping, splicing and polyadenylation. In addition, their function also critically depends on proper localization -- sometimes trafficking to the remote parts of the cell such as dendrites and axons of neurons -- and proper control of their stability. Furthermore, thousands of long and small noncoding RNAs are produced to play a wide range of roles in gene regulation. From our perspective, two overarching goals for RNA biology include （i） characterizing the spatial-temporal regulation of various RNA species and elucidating the underlying regulatory mechanisms; （ii） understanding the functional impact of such regulation on human physiology and disease.

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