ISBRA 2023: THE 19TH INTERNATIONAL SYMPOSIUM ON BIOINFORMATICS RESEARCH AND APPLICATIONS

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Ahmed, Sheraz	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Ali, Sarwan	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection PDB2Vec: Using 3D Structural Information For Improved Protein Analysis Sequence-Based Nanobody-Antigen Binding Prediction
An, Ying	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Andersen, Jakob Lykke	Reconciling Inconsistent Molecular Structures from Biochemical Databases On the Realisability of Chemical Pathways
Annan, Richard	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
Asim, Muhammad Nabeel	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Ayub, Muhammad Sohaib	Sequence-Based Nanobody-Antigen Binding Prediction
B
Banke, Sissel	On the Realisability of Chemical Pathways
Bansal, Mukul S.	Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
Bao, Jinku	PDFll: Intrinsic protein disorder and function prediction from the language of life
Basak, Joyanta	On Computing the Jaro Similarity Between Two Strings
Bashir, Khurram	Sequence-Based Nanobody-Antigen Binding Prediction
Bi, Xingyu	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
Bi, Xuehua	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Bleker, Carissa	A Brief Study of Gene Co-Expression Thresholding Algorithms
Bolteau, Mathieu	Inferring Boolean networks from single-cell human embryo datasets
Bourdon, Jérémie	Inferring Boolean networks from single-cell human embryo datasets
C
Cao, Chen	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Celms, Edgars	Clique-based topological characterization of chromatin interaction hubs
Chen, Fan	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Chen, Ming	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Chen, Pin-Yu	Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences
Chourasia, Prakash	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection PDB2Vec: Using 3D Structural Information For Improved Protein Analysis
Comin, Matteo	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
Cui, Guosheng	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Czech, Bartosz	The effect of transcriptomic annotations in breast cancer DGE study
D
Dai, Ling-Yun	scGASI: A graph autoencoder-based single-cell integration clustering method
David, Laurent	Inferring Boolean networks from single-cell human embryo datasets
Dengel, Andreas	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Deo, Nachiket	On Computing the Jaro Similarity Between Two Strings
Dias, Zanoni	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Duan, Xiaohong	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
E
Eriksen, Casper Asbjørn	Reconciling Inconsistent Molecular Structures from Biochemical Databases
F
Fagerberg, Rolf	Reconciling Inconsistent Molecular Structures from Biochemical Databases On the Realisability of Chemical Pathways
Farooq, Hafsa	Genetic Algorithm with Evolutionary Jumps
Fazeel, Ahtisham	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
Feng, Hui	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Feng, Shengzhong	PCPI: Prediction of circRNA and protein interaction using machine learning method
Fernandes, Francisco	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
Fertin, Guillaume	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Flamm, Christoph	On the Realisability of Chemical Pathways
Freitas, Ana Teresa	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
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Gao, Rui	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
Gao, Yajun	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Grady, Stephen	A Brief Study of Gene Co-Expression Thresholding Algorithms
Guan, Boxin	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Guan, Yuxia	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion
Guo, Fengyi	MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion
Guo, Lin	DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Guziolowski, Carito	Inferring Boolean networks from single-cell human embryo datasets
H
Haase, Kenneth	On Computing the Jaro Similarity Between Two Strings
Han, Renmin	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
He, Jian	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
He, Jiayin	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Hofacker, Ivo	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Hossain, Md. Tofazzal	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics PCPI: Prediction of circRNA and protein interaction using machine learning method
Hou, Xiaodi	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Hu, Jifang	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Hu, Taiyuan	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Hu, Zitao	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Huang, Huazhen	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
I
Ionov, Yurij	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
J
Jean, Géraldine	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Ji, Chunyan	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Ji, Detao	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Jiang, Chunyang	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Jiang, Haitao	On Sorting by Flanked Transpositions
Ju, Zhen	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Juyal, Akshay	Genetic Algorithm with Evolutionary Jumps Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
K
Kang, Liping	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
Katriel, Guy	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Keliang, Zhao	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
Khan, Imdadullah	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification Sequence-Based Nanobody-Antigen Binding Prediction
Kong, Xiang-Zhen	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Koutschan, Christoph	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
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Lace, Lelde	Clique-based topological characterization of chromatin interaction hubs
Langston, Michael A.	A Brief Study of Gene Co-Expression Thresholding Algorithms
Lavor, Carlile	The Ordered Covering Problem in Distance Geometry
Lei, Hongyang	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Lei, Xiujuan	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Li, Feng	scGASI: A graph autoencoder-based single-cell integration clustering method ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Li, Hongjia	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Li, Ruilin	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Li, Sheng-Jun	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Li, Xiaobo	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Li, Yahan	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Li, Ye	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Li, Yulong	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Lin, Haixiang	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Liu, Jin	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Liu, Jin-Xing	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Liu, Qin	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Liu, Xiaowen	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
Liu, Xin	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Liu, Zhi	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Liu, Zixue	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
Lorenz, Ronny	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Luan, Haijing	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Lv, Ya	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
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Ma, Bin	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
Ma, Huidong	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Mahanaymi, Udi	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Maia, Nilton	The Ordered Covering Problem in Distance Geometry
Mansoor, Haris	Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification
Mathur, Anup	On Computing the Jaro Similarity Between Two Strings
Melkus, Gatis	Clique-based topological characterization of chromatin interaction hubs
Meng, Jintao	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
Meng, Mei	Neurogenesis-associated Protein, a Potential Prognostic Biomarker in anti-PD-1 based kidney renal clear cell carcinoma patients therapeutics
Merkle, Daniel	Reconciling Inconsistent Molecular Structures from Biochemical Databases On the Realisability of Chemical Pathways
Mielczarek, Magda	The effect of transcriptomic annotations in breast cancer DGE study
Murad, Taslim	Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection
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Niu, Beifang	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Niyogisubizo, Jovial	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
Novikov, Daniel	Genetic Algorithm with Evolutionary Jumps
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Oliveira Alexandrino, Alexsandro	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
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Pan, Yi	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Park, Krista	On Computing the Jaro Similarity Between Two Strings
Patterson, Murray	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification Unveiling the Robustness of Machine Learning Models in Classifying COVID-19 Spike Sequences Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs Hist2Vec: Kernel-Based Embeddings for Biological Sequence Classification Enhancing t-SNE Performance for Biological Sequencing Data through Kernel Selection PDB2Vec: Using 3D Structural Information For Improved Protein Analysis Sequence-Based Nanobody-Antigen Binding Prediction
Peng, Yin	PCPI: Prediction of circRNA and protein interaction using machine learning method
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Qiao, Tian-Jing	scGASI: A graph autoencoder-based single-cell integration clustering method
Qingge, Letu	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
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Rajasekaran, Sanguthevar	On Computing the Jaro Similarity Between Two Strings
Reza, Md. Selim	PCPI: Prediction of circRNA and protein interaction using machine learning method
Rodrigues Oliveira, Andre	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Rosiyadi, Didi	Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images
Rossignolo, Enrico	USTAR: Improved Compression of k-mer Sets with Counters Using De Bruijn Graphs
Rucevskis, Peteris	Clique-based topological characterization of chromatin interaction hubs
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Saghaian, Hossein	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Sahni, Sartaj	On Computing the Jaro Similarity Between Two Strings
Sahoo, Bikram	Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms
Salgado, André	CSA-MEM: Enhancing Circular DNA Multiple Alignment through Text Indexing Algorithms
Sang, Guoming	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Sardar, Usama	Efficient Sequence Embedding For SARS-CoV-2 Variants Classification Sequence-Based Nanobody-Antigen Binding Prediction
Shang, Junliang	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Shoaib, Muhammad	Sequence-Based Nanobody-Antigen Binding Prediction
Siliņa, Sandra	Clique-based topological characterization of chromatin interaction hubs
Siqueira, Gabriel	Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
Sizovs, Andrejs	Clique-based topological characterization of chromatin interaction hubs
Skums, Pavel	Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire
Snir, Sagi	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Soliman, Ahmed	On Computing the Jaro Similarity Between Two Strings
Souza, Michael	The Ordered Covering Problem in Distance Geometry
Spicher, Thomas	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Stadler, Peter F.	On the Realisability of Chemical Pathways Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Steel, Mike	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Steorts, Rebecca	On Computing the Jaro Similarity Between Two Strings
Sturtz, Jordan	A Convolutional Denoising Autoencoder for Protein Scaffold Filling
Stępień, Rafał	The effect of transcriptomic annotations in breast cancer DGE study
Sun, Hui	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Szyda, Joanna	The effect of transcriptomic annotations in breast cancer DGE study
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Tang, Panrui	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Tayebi, Zahra	Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
Tong, Xin	On Sorting by Flanked Transpositions
Trygg, Johan	Deep Learning Architectures For the Prediction of YY1-Mediated Chromatin Loops
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Varenyk, Yuliia	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Viksna, Juris	Clique-based topological characterization of chromatin interaction hubs
von Loehneysen, Sarah	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
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Wang, Anqi	ABCAE: Artificial Bee Colony Algorithm with Adaptive Exploitation for Epistatic Interaction Detection
Wang, Guishen	BiRNN-DDI:A Drug-drug Interaction Event Type Prediction Model based on Bidirectional Recurrent Neural Network and Graph to Sequence Representation
Wang, Jianxin	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge MPFNet: ECG Arrhythmias Classication Based on Multi-Perspective Feature Fusion
Wang, Juan	scGASI: A graph autoencoder-based single-cell integration clustering method CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Wang, Lusheng	On Sorting by Flanked Transpositions
Wang, Ruxin	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Wang, Shaokai	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry
Wang, Tai-Ge	CHLPCA: Correntropy-Based Hypergraph Regularized Sparse PCA for Single-cell Type Identification
Wang, Xiaowen	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Wei, Yanjie	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics Attention-Guided Residual U-Net with SE Connection and ASPP for Watershed-based Cell Segmentation in Microscopy Images PCPI: Prediction of circRNA and protein interaction using machine learning method
Weinberg, Daniel	On Computing the Jaro Similarity Between Two Strings
Wu, Chuanfang	PDFll: Intrinsic protein disorder and function prediction from the language of life
Wu, Dan	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Wu, Xiaohui	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
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Xi, Wenhui	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Xiong, Anxuan	DCNN: Dual-Level Collaborative Neural Network for Imbalanced Heart Anomaly Detection
Xu, Huixiu	On Sorting by Flanked Transpositions
Xu, Shuo	Integrative analysis of gene expression and alternative polyadenylation from single-cell RNA-seq data
Y
Yan, Cheng	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Yang, Bokai	TCSA: A Text-guided Cross-view Medical Semantic Alignment Framework for Adaptive Multi-view Visual Representation Learning
Yang, Chunyan	Multi-Class Cancer Classification of Whole Slide Images through Transformer and Multiple Instance Learning
Yang, Pei	Multi-modality MRI Feature Interaction for Pseudoprogression Prediction of Glioblastoma
Yang, Wanyi	PDFll: Intrinsic protein disorder and function prediction from the language of life
Yang, Zhidong	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Yao, Bin	Predicting Comprehensive Drug-Drug Interactions by Magnetic Signed Graph Neural Network
Yao, Hua-Ting	Phylogenetic Information as Soft Constraints in RNA Secondary Structure Prediction
Yuan, Shasha	scGASI: A graph autoencoder-based single-cell integration clustering method
Z
Zaman, Sumaira	Reducing the impact of domain rearrangement on sequence alignment and phylogeny reconstruction
Zang, Dawei	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Zeilberger, Doron	Using Generating Functions to Prove Additivity of Gene-Neighborhood Based Phylogenetics
Zelikovsky, Alex	Genetic Algorithm with Evolutionary Jumps Graph-Based Motif Discovery in Mimotope Profiles of Serum Antibody Repertoire Deep Learning Reveals Biological Basis of Racial Disparities in Quadruple-Negative Breast Cancer Exploring Racial Disparities in Triple-Negative Breast Cancer: Insights from Feature Selection Algorithms Simulating tumor evolution from scDNA-seq as an accumulation of both SNVs and CNAs
Zhang, Fa	SaID: Simulation-aware Image Denoising Pre-trained Model for Cryo-EM Micrographs
Zhang, Jingjing	Identification and functional annotation of circRNAs in neuroblastoma based on bioinformatics
Zhang, Linlin	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Zhang, Yan	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Zhang, Yijia	Radiology Report Generation via Visual Recalibration and Context Gating-aware
Zhang, Zuping	SGMDD: Subgraph Neural Network-Based Model for Analyzing Functional Connectivity Signatures of Major Depressive Disorder
Zhao, Kai	Identifying miRNA-disease Associations based on Simple Graph Convolution with DropMessage and Jumping Knowledge
Zhong, Cheng	ricME: long-read based mobile element variant detection using sequence realignment and identity calculation
Zhu, Binhai	A Convolutional Denoising Autoencoder for Protein Scaffold Filling On Sorting by Flanked Transpositions
Zhu, Daming	On Sorting by Flanked Transpositions
Zhu, Hongming	HetBiSyn: Predicting Anticancer Synergistic Drug Combinations Featuring Bi-perspective Drug Embedding with Heterogeneous Data
Zhu, Ming	NeoMS: Identification of Novel MHC-I Peptides with Tandem Mass Spectrometry

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