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ORCIDIEEE/ACM Transactions on Computational Biology and Bioinformatics, Volume 19
Volume 19, Number 1, January - February 2022
- Hsiao-Fang Sunny Sun
, Yi-Ping Phoebe Chen:
Editorial. 1-2 - Hui Bi, Shumei Cao, Hanying Yan, Zhongyi Jiang, Jun Zhang, Ling Zou:
Resting State Functional Connectivity Analysis During General Anesthesia: A High-Density EEG Study. 3-13 - Pierrick Craveur, Tarun J. Narwani, Narayanaswamy Srinivasan, Jean-Christophe Gelly, Joseph Rebehmed, Alexandre G. de Brevern:
Shaking the β-Bulges. 14-18 - Madhusudan Paul, Ashish Anand:
A New Family of Similarity Measures for Scoring Confidence of Protein Interactions Using Gene Ontology. 19-30 - Runhua Huang, Chengchuang Lin, Aihua Yin, Hanbiao Chen, Li Guo, Gansen Zhao, Xiaomao Fan, Shuangyin Li, Jinji Yang:
A Clinical Dataset and Various Baselines for Chromosome Instance Segmentation. 31-39 - Ying Qian, Xuelian Li, Qian Zhang, Jiongmin Zhang:
SPP-CPI: Predicting Compound-Protein Interactions Based On Neural Networks. 40-47 - Jin Zhao, Haodi Feng, Daming Zhu, Yu Lin:
MultiTrans: An Algorithm for Path Extraction Through Mixed Integer Linear Programming for Transcriptome Assembly. 48-56 - Anuradha Wickramarachchi, Yu Lin:
GraphPlas: Refined Classification of Plasmid Sequences Using Assembly Graphs. 57-67 - Shuai Lu, Yuguang Li, Fei Wang, Xiaofei Nan, Shoutao Zhang:
Leveraging Sequential and Spatial Neighbors Information by Using CNNs Linked With GCNs for Paratope Prediction. 68-74 - Tzu-Hsien Yang:
An Aggregation Method to Identify the RNA Meta-Stable Secondary Structure and its Functionally Interpretable Structure Ensemble. 75-86 - Trinh-Trung-Duong Nguyen, The-Anh Tran, Nguyen-Quoc-Khanh Le, Dinh-Minh Pham, Yu-Yen Ou:
An Extensive Examination of Discovering 5-Methylcytosine Sites in Genome-Wide DNA Promoters Using Machine Learning Based Approaches. 87-94 - Barbara Di Camillo, Giuseppe Nicosia:
Guest Editorial: Deep Learning For Genomics. 95-96 - Jim Clauwaert, Willem Waegeman:
Novel Transformer Networks for Improved Sequence Labeling in genomics. 97-106 - Zhong Chen, Wensheng Zhang, Hong-Wen Deng, Kun Zhang:
Effective Cancer Subtype and Stage Prediction via Dropfeature-DNNs. 107-120 - Francisco Cristovao, Silvia Cascianelli, Arif Canakoglu, Mark J. Carman, Luca Nanni, Pietro Pinoli, Marco Masseroli:
Investigating Deep Learning Based Breast Cancer Subtyping Using Pan-Cancer and Multi-Omic Data. 121-134 - Gautier Viaud, Prasanna Mayilvahanan, Paul-Henry Cournède:
Representation Learning for the Clustering of Multi-Omics Data. 135-145 - Tuan Nguyen, Giang T. T. Nguyen, Thin Nguyen, Duc-Hau Le:
Graph Convolutional Networks for Drug Response Prediction. 146-154 - Satyajit Mahapatra, Vivek Raj Gupta, Sitanshu Sekhar Sahu, Ganapati Panda:
Deep Neural Network and Extreme Gradient Boosting Based Hybrid Classifier for Improved Prediction of Protein-Protein Interaction. 155-165 - Zhipeng Cai, Min Li, Pavel Skums:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 166-167 - Cheng Yan, Guihua Duan, Yayan Zhang, Fang-Xiang Wu, Yi Pan, Jianxin Wang:
Predicting Drug-Drug Interactions Based on Integrated Similarity and Semi-Supervised Learning. 168-179 - Fengpan Zhao, Pavel Skums, Alex Zelikovsky, Eric L. Sevigny, Monica Haavisto Swahn, Sheryl M. Strasser, Yan Huang, Yubao Wu:
Computational Approaches to Detect Illicit Drug Ads and Find Vendor Communities Within Social Media Platforms. 180-191 - Sudipta Acharya, Laizhong Cui, Yi Pan:
A Refined 3-in-1 Fused Protein Similarity Measure: Application in Threshold-Free Hub Detection. 192-206 - Zhipeng Cai, Giri Narasimhan, Pavel Skums:
Guest Editors' Introduction to the Special Section on Bioinformatics Research and Applications. 207-208 - Shan Gao, Renmin Han, Xiangrui Zeng, Zhiyong Liu, Min Xu, Fa Zhang:
Macromolecules Structural Classification With a 3D Dilated Dense Network in Cryo-Electron Tomography. 209-219 - Davide Storato, Matteo Comin:
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification. 220-229 - Saurav Dhar, Chengchen Zhang, Ion I. Mandoiu, Mukul S. Bansal:
TNet: Transmission Network Inference Using Within-Host Strain Diversity and its Application to Geographical Tracking of COVID-19 Spread. 230-242 - Jun Wang, Huiling Zhang, Wei Ren, Maozu Guo, Guoxian Yu:
EpiMC: Detecting Epistatic Interactions Using Multiple Clusterings. 243-254 - P. V. Sunil Kumar, Adheeba Thahsin, Manju M, G. Gopakumar:
A Heterogeneous Information Network Model for Long Non-Coding RNA Function Prediction. 255-266 - Hansheng Li, Jianping Li, Yuxin Kang, Chunbao Wang, Feihong Liu, Wenli Hui, Qirong Bo, Lei Cui, Jun Feng, Lin Yang:
A Novel Encoding and Decoding Calibration Guiding Pathway for Pathological Image Analysis. 267-274 - Sadaf Gull, Fayyaz A. Minhas:
AMP0: Species-Specific Prediction of Anti-microbial Peptides Using Zero and Few Shot Learning. 275-283 - Mahdi Pursalim, Kwoh Chee Keong:
An Efficient Multiresolution Clustering for Motif Discovery in Complex Networks. 284-294 - Yuning Yang, Jiawen Yu, Zhe Liu, Xi Wang, Han Wang, Zhiqiang Ma, Dong Xu:
An Improved Topology Prediction of Alpha-Helical Transmembrane Protein Based on Deep Multi-Scale Convolutional Neural Network. 295-304 - Xiaoke Ma, Peng Gang Sun, Maoguo Gong:
An Integrative Framework of Heterogeneous Genomic Data for Cancer Dynamic Modules Based on Matrix Decomposition. 305-316 - Fei Liu, Ena Yamamoto, Katsunobu Shirahama, Tsubasa Saitoh, Shuhei Aoyama, Yumiko Harada, Ryutaro Murakami, Hiroshi Matsuno:
Analysis of Pattern Formation by Colored Petri Nets With Quantitative Regulation of Gene Expression Level. 317-327 - Sanzo Miyazawa:
Boltzmann Machine Learning and Regularization Methods for Inferring Evolutionary Fields and Couplings From a Multiple Sequence Alignment. 328-342 - Devleena Ghosh, Chittaranjan Mandal:
Clustering Based Parameter Estimation of Thyroid Hormone Pathway. 343-354 - Rubén Langarita, Adrià Armejach, Javier Setoain, Pablo Ibáñez-Marín, Jesús Alastruey-Benedé, Miquel Moretó:
Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps. 355-368 - Md. Rezaul Karim, Michael Cochez, Achille Zappa, Ratnesh Sahay, Dietrich Rebholz-Schuhmann, Oya Beyan, Stefan Decker:
Convolutional Embedded Networks for Population Scale Clustering and Bio-Ancestry Inferencing. 369-382 - Rizwan Qureshi, Avirup Ghosh, Hong Yan:
Correlated Motions and Dynamics in Different Domains of Epidermal Growth Factor Receptor With L858R and T790M Mutations. 383-394 - Chunxiang Peng, Xiao-Gen Zhou, Gui-Jun Zhang:
De novo Protein Structure Prediction by Coupling Contact With Distance Profile. 395-406 - Mohammad A. Rezaei, Yanjun Li, Dapeng Wu, Xiaolin Li, Chenglong Li:
Deep Learning in Drug Design: Protein-Ligand Binding Affinity Prediction. 407-417 - Anju Sharma, Rajnish Kumar, Rahul Semwal, Imlimaong Aier, Pankaj Tyagi, Pritish Kumar Varadwaj:
DeepOlf: Deep Neural Network Based Architecture for Predicting Odorants and Their Interacting Olfactory Receptors. 418-428 - Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler:
Generic Context-Aware Group Contributions. 429-442 - Rituparna Sinha, Rajat Kumar Pal, Rajat K. De:
GenSeg and MR-GenSeg: A Novel Segmentation Algorithm and its Parallel MapReduce Based Approach for Identifying Genomic Regions With Copy Number Variations. 443-454 - Chang Sun, Ping Xuan, Tiangang Zhang, Yilin Ye:
Graph Convolutional Autoencoder and Generative Adversarial Network-Based Method for Predicting Drug-Target Interactions. 455-464 - Kiya Govek, Camden Sikes, Yangqiaoyu Zhou, Layla Oesper:
GraPhyC: Using Consensus to Infer Tumor Evolution. 465-478 - Peng Peng, Yipu Zhang, Yongfeng Ju, Kaiming Wang, Gang Li, Vince D. Calhoun, Yu-Ping Wang:
Group Sparse Joint Non-Negative Matrix Factorization on Orthogonal Subspace for Multi-Modal Imaging Genetics Data Analysis. 479-490 - Ozlem Muslu, Charles Tapley Hoyt, Mauricio Lacerda, Martin Hofmann-Apitius, Holger Fröhlich:
GuiltyTargets: Prioritization of Novel Therapeutic Targets With Network Representation Learning. 491-500 - Sai Zhang, Jin Li, Wei Zhou, Tong Li, Yang Zhang, Jingru Wang:
Higher-Order Proximity-Based MiRNA-Disease Associations Prediction. 501-512 - Yuting Tan, Le Ou-Yang, Xingpeng Jiang, Hong Yan, Xiao-Fei Zhang:
Identifying Gene Network Rewiring Based on Partial Correlation. 513-521 - Samet Tenekeci, Zerrin Isik:
Integrative Biological Network Analysis to Identify Shared Genes in Metabolic Disorders. 522-530 - Anup Kumar Halder, Soumyendu Sekhar Bandyopadhyay, Piyali Chatterjee, Mita Nasipuri, Dariusz Plewczynski, Subhadip Basu:
JUPPI: A Multi-Level Feature Based Method for PPI Prediction and a Refined Strategy for Performance Assessment. 531-542 - Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri:
META-BASE: A Novel Architecture for Large-Scale Genomic Metadata Integration. 543-557 - Eunji Kim, Ivan Ivanov, Edward R. Dougherty:
Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network - A Boolean Network Modeling Perspective. 558-568 - Yajun Dai, Yang Li, Liping Wang, Zhenling Peng, Jianyi Yang:
On Monomeric and Multimeric Structures-Based Protein-Ligand Interactions. 569-574 - Kuo Yang, Yi Zheng, Kezhi Lu, Kai Chang, Ning Wang, Zixin Shu, Jian Yu, Baoyan Liu, Zhuye Gao, Xuezhong Zhou:
PDGNet: Predicting Disease Genes Using a Deep Neural Network With Multi-View Features. 575-584 - Rahul Semwal, Imlimaong Aier, Utkarsh Raj, Pritish Kumar Varadwaj:
Pr[m]: An Algorithm for Protein Motif Discovery. 585-592 - Wei Zhong, Feng Gu:
Predicting Local Protein 3D Structures Using Clustering Deep Recurrent Neural Network. 593-604 - Dewu Ding, Xiao Sun:
Relating Translation Efficiency to Protein Networks Provides Evolutionary Insights in Shewanella and Its Implications for Extracellular Electron Transfer. 605-613 - Neng Huang, Fan Nie, Peng Ni, Feng Luo, Jianxin Wang:
SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism. 614-623 - Priyadarshini Rai, Debarka Sengupta, Angshul Majumdar:
SelfE: Gene Selection via Self-Expression for Single-Cell Data. 624-632 - Yan Liu, Hao Liang, Quan Zou, Zengyou He:
Significance-Based Essential Protein Discovery. 633-642 - Qiao Ning, Zhiqiang Ma, Xiaowei Zhao, Minghao Yin:
SSKM_Succ: A Novel Succinylation Sites Prediction Method Incorporating K-Means Clustering With a New Semi-Supervised Learning Algorithm. 643-652
Volume 19, Number 2, March - April 2022
- Pietro Hiram Guzzi, Marinka Zitnik:
Editorial Deep Learning and Graph Embeddings for Network Biology. 653-654 - Jin Li, Jingru Wang, Hao Lv, Zhuoxuan Zhang, Zaixia Wang:
IMCHGAN: Inductive Matrix Completion With Heterogeneous Graph Attention Networks for Drug-Target Interactions Prediction. 655-665 - Xiaoyong Pan, Lei Chen, Min Liu, Zhibin Niu, Tao Huang, Yu-Dong Cai:
Identifying Protein Subcellular Locations With Embeddings-Based node2loc. 666-675 - Kishan KC, Rui Li, Feng Cui, Anne R. Haake:
Predicting Biomedical Interactions With Higher-Order Graph Convolutional Networks. 676-687 - Xiujuan Lei, Jiaojiao Tie, Yi Pan:
Inferring Metabolite-Disease Association Using Graph Convolutional Networks. 688-698 - Jianliang Gao, Tengfei Lyu, Fan Xiong, Jianxin Wang, Weimao Ke, Zhao Li:
Predicting the Survival of Cancer Patients With Multimodal Graph Neural Network. 699-709 - Giang T. T. Nguyen, Hoa D. Vu, Duc-Hau Le:
Integrating Molecular Graph Data of Drugs and Multiple -Omic Data of Cell Lines for Drug Response Prediction. 710-717 - Tri Minh Nguyen, Thin Nguyen, Thao Minh Le, Truyen Tran:
GEFA: Early Fusion Approach in Drug-Target Affinity Prediction. 718-728 - Ichcha Manipur, Mario Manzo, Ilaria Granata, Maurizio Giordano, Lucia Maddalena, Mario R. Guarracino:
Netpro2vec: A Graph Embedding Framework for Biomedical Applications. 729-740 - Yuanfang Ren, Aisharjya Sarkar, Pierangelo Veltri, Ahmet Ay, Alin Dobra, Tamer Kahveci:
Pattern Discovery in Multilayer Networks. 741-752 - Zhen Shen, Qinhu Zhang, Kyungsook Han, De-Shuang Huang:
A Deep Learning Model for RNA-Protein Binding Preference Prediction Based on Hierarchical LSTM and Attention Network. 753-762 - Zhen Gao, Yu-Tian Wang, Qing-Wen Wu, Lei Li, Jian-Cheng Ni, Chun-Hou Zheng:
A New Method Based on Matrix Completion and Non-Negative Matrix Factorization for Predicting Disease-Associated miRNAs. 763-772 - Koushik Mallick, Saurav Mallik, Sanghamitra Bandyopadhyay, Sikim Chakraborty:
A Novel Graph Topology-Based GO-Similarity Measure for Signature Detection From Multi-Omics Data and its Application to Other Problems. 773-785 - Xin Huang, Zhenqian Liao, Bing Liu, Fengmei Tao, Benzhe Su, Xiaohui Lin:
A Novel Method for Constructing Classification Models by Combining Different Biomarker Patterns. 786-794 - Shi-Hao Feng, Chun-Qiu Xia, Pei-Dong Zhang, Hong-Bin Shen:
Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks. 795-805 - Trinh Van Giang, Tatsuya Akutsu, Kunihiko Hiraishi:
An FVS-Based Approach to Attractor Detection in Asynchronous Random Boolean Networks. 806-818 - Yiding Zhang, Lyujie Chen, Shao Li:
CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data. 819-829 - Aisharjya Sarkar, Prabhat Mishra, Tamer Kahveci:
Data Perturbation and Recovery of Time Series Gene Expression Data. 830-842 - Sachin Bhatt, Prithvi Singh, Archana Sharma, Arpita Rai, Ravins Dohare, Shweta Sankhwar, Akash Sharma, Mansoor Ali Syed:
Deciphering Key Genes and miRNAs Associated With Hepatocellular Carcinoma via Network-Based Approach. 843-853 - Yuting Su, Yao Lu, Mei Chen, An-An Liu:
Deep Reinforcement Learning-Based Progressive Sequence Saliency Discovery Network for Mitosis Detection In Time-Lapse Phase-Contrast Microscopy Images. 854-865 - Ben Cao, Xue Ii, Xiaokang Zhang, Bin Wang, Qiang Zhang, Xiaopeng Wei:
Designing Uncorrelated Address Constrain for DNA Storage by DMVO Algorithm. 866-877 - Boxin Guan, Yuhai Zhao, Ying Yin, Yuan Li:
Detecting Disease-Associated SNP-SNP Interactions Using Progressive Screening Memetic Algorithm. 878-887 - Ho Bae, Seonwoo Min, Hyun-Soo Choi, Sungroh Yoon:
DNA Privacy: Analyzing Malicious DNA Sequences Using Deep Neural Networks. 888-898 - Seonho Kim, Juntae Yoon:
Dual Triggered Correspondence Topic (DTCT)model for MeSH annotation. 899-911 - Christian Ponte-Fernández, Jorge González-Domínguez, Antonio Carvajal-Rodríguez, María J. Martín:
Evaluation of Existing Methods for High-Order Epistasis Detection. 912-926 - Tapan Chowdhury, Susanta Chakraborty, Argha Nandan:
GPU Accelerated Drug Application on Signaling Pathways Containing Multiple Faults Using Boolean Networks. 927-939 - Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mark Kunitomi, Mary Roth, Vandana V. Mukherjee, James H. Kaufman:
Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale. 940-952 - Fei Wang, Yulian Ding, Xiujuan Lei, Bo Liao, Fang-Xiang Wu:
Identifying Gene Signatures for Cancer Drug Repositioning Based on Sample Clustering. 953-965 - Meshari Alazmi, Olaa A. Motwalli:
Immuno-Informatics Based Peptides: An Approach for Vaccine Development Against Outer Membrane Proteins of Pseudomonas Genus. 966-973 - Khalique Newaz, Tijana Milenkovic:
Inference of a Dynamic Aging-related Biological Subnetwork via Network Propagation. 974-988 - Guobo Xie, Jiawei Jiang, Yuping Sun:
LDA-LNSUBRW: lncRNA-Disease Association Prediction Based on Linear Neighborhood Similarity and Unbalanced bi-Random Walk. 989-997 - Lijun Quan, Xiaoyu Sun, Jian Wu, Jie Mei, Liqun Huang, Ruji He, Liangpeng Nie, Yu Chen, Qiang Lyu:
Learning Useful Representations of DNA Sequences From ChIP-Seq Datasets for Exploring Transcription Factor Binding Specificities. 998-1008 - Daniele Tavernelli, Tiziana Calamoneri, Paola Vocca:
Linear Time Reconciliation With Bounded Transfers of Genes. 1009-1017 - Bin Wang, Yongsheng Gao, Xiaohui Yuan, Shengwu Xiong:
Local R-Symmetry Co-Occurrence: Characterising Leaf Image Patterns for Identifying Cultivars. 1018-1031 - Nikhilanand Arya, Sriparna Saha:
Multi-Modal Classification for Human Breast Cancer Prognosis Prediction: Proposal of Deep-Learning Based Stacked Ensemble Model. 1032-1041 - Haonan Feng, Ruiqing Zheng, Jianxin Wang, Fang-Xiang Wu, Min Li:
NIMCE: A Gene Regulatory Network Inference Approach Based on Multi Time Delays Causal Entropy. 1042-1049 - Liliana Ironi, Ettore Lanzarone:
Optimal Robust Search for Parameter Values of Qualitative Models of Gene Regulatory Networks. 1050-1063 - Hua Zhang, Guogen Shan, Bailin Yang:
Optimized Elastic Network Models With Direct Characterization of Inter-Residue Cooperativity for Protein Dynamics. 1064-1074 - Xiangan Chen, Shuai Liu, Wen Zhang:
Predicting Coding Potential of RNA Sequences by Solving Local Data Imbalance. 1075-1083 - Jianhong Cheng, Jin Liu, Hailin Yue, Harrison Bai, Yi Pan, Jianxin Wang:
Prediction of Glioma Grade Using Intratumoral and Peritumoral Radiomic Features From Multiparametric MRI Images. 1084-1095 - Nishtha Hooda, Ruchika Gupta, Nidhi Rani Gupta:
Prediction of Malignant Breast Cancer Cases Using Ensemble Machine Learning: A Case Study of Pesticides Prone Area. 1096-1104 - Shweta Yadav, Srivatsa Ramesh Jayashree, Sriparna Saha, Asif Ekbal:
Relation Extraction From Biomedical and Clinical Text: Unified Multitask Learning Framework. 1105-1116 - Subin Qian, Huiyi Liu, Xiaofeng Yuan, Wei Wei, Shuangshuang Chen, Hong Yan:
Row and Column Structure-Based Biclustering for Gene Expression Data. 1117-1129 - Ekta Shah, Pradipta Maji:
Scalable Non-Linear Graph Fusion for Prioritizing Cancer-Causing Genes. 1130-1143 - Zhijie Ni, Xiaoying Zheng, Xiao Zheng, Xiufen Zou:
scLRTD : A Novel Low Rank Tensor Decomposition Method for Imputing Missing Values in Single-Cell Multi-Omics Sequencing Data. 1144-1153 - Chuan-Yuan Wang, Ying-Lian Gao, Jin-Xing Liu, Xiang-Zhen Kong, Chun-Hou Zheng:
Single-Cell RNA Sequencing Data Clustering by Low-Rank Subspace Ensemble Framework. 1154-1164 - Jason L. Causey, Keyu Li, Xianghao Chen, Wei Dong, Karl Walker, Jake A. Qualls, Jonathan Stubblefield, Jason H. Moore, Yuanfang Guan, Xiuzhen Huang:
Spatial Pyramid Pooling With 3D Convolution Improves Lung Cancer Detection. 1165-1172 - Andri Mirzal:
Statistical Analysis of Microarray Data Clustering using NMF, Spectral Clustering, Kmeans, and GMM. 1173-1192 - Cheng Liu, Wenming Cao, Si Wu, Wenjun Shen, Dazhi Jiang, Zhiwen Yu, Hau-San Wong:
Supervised Graph Clustering for Cancer Subtyping Based on Survival Analysis and Integration of Multi-Omic Tumor Data. 1193-1202