0 | -- | 0 | Hukam Chand Rawal, Shakir Ali, Tapan Kumar Mondal. miRPreM and tiRPreM: Improved methodologies for the prediction of miRNAs and tRNA-induced small non-coding RNAs for model and non-model organisms |
0 | -- | 0 | Chun-Chun Wang, Chi-Chi Zhu, Xing Chen 0001. Ensemble of kernel ridge regression-based small molecule-miRNA association prediction in human disease |
0 | -- | 0 | Menglu Li, Wen Zhang. PHIAF: prediction of phage-host interactions with GAN-based data augmentation and sequence-based feature fusion |
0 | -- | 0 | Kamil Kaminski, Jan Ludwiczak, Maciej Jasinski, Adriana Bukala, Rafal Madaj, Krzysztof Szczepaniak, Stanislaw Dunin-Horkawicz. Rossmann-toolbox: a deep learning-based protocol for the prediction and design of cofactor specificity in Rossmann fold proteins |
0 | -- | 0 | Lirong Zhang, Yanchao Yang, Lu Chai, Qianzhong Li, Junjie Liu, Hao Lin 0001, Li Liu. A deep learning model to identify gene expression level using cobinding transcription factor signals |
0 | -- | 0 | Sander N. Goossens, Tim H. Heupink, Elise De Vos, Anzaan Dippenaar, Margaretha De Vos, Rob Warren, Annelies Van Rie. Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data |
0 | -- | 0 | Ke Han, Long-Chen Shen, Yi-Heng Zhu, Jian Xu, Jiangning Song, Dong-jun Yu. MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network |
0 | -- | 0 | Vishakha Singh, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar 0003, Sonal Saxena. StaBle-ABPpred: a stacked ensemble predictor based on biLSTM and attention mechanism for accelerated discovery of antibacterial peptides |
0 | -- | 0 | Quang-Thai Ho, Nguyen-Quoc-Khanh Le, Yu-Yen Ou. mCNN-ETC: identifying electron transporters and their functional families by using multiple windows scanning techniques in convolutional neural networks with evolutionary information of protein sequences |
0 | -- | 0 | Siqi Bao, Ke Li, Congcong Yan, Zicheng Zhang, Jia Qu, Meng Zhou 0003. Deep learning-based advances and applications for single-cell RNA-sequencing data analysis |
0 | -- | 0 | Francesco Napolitano, Xiaopeng Xu, Xin Gao 0001. Impact of computational approaches in the fight against COVID-19: an AI guided review of 17 000 studies |
0 | -- | 0 | María Virginia Sabando, Ignacio Ponzoni, Evangelos E. Milios, Axel J. Soto. Using molecular embeddings in QSAR modeling: does it make a difference? |
0 | -- | 0 | Haoxiang Qin, Qidong Shen, Hongyi Zhao, Guozhen Qi, Lei Gao. Network-based analysis revealed significant interactions between risk genes of severe COVID-19 and host genes interacted with SARS-CoV-2 proteins |
0 | -- | 0 | Rong Tang, Zijian Wu, Zeyin Rong, Jin Xu, Wei Wang, Bo Zhang, Xianjun Yu, Si Shi. Ferroptosis-related lncRNA pairs to predict the clinical outcome and molecular characteristics of pancreatic ductal adenocarcinoma |
0 | -- | 0 | Yongxian Fan, Meijun Chen, Xiaoyong Pan. GCRFLDA: scoring lncRNA-disease associations using graph convolution matrix completion with conditional random field |
0 | -- | 0 | Shuangquan Zhang, Anjun Ma, Jing Zhao, Dong Xu, Qin Ma 0003, Yan Wang 0028. Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data |
0 | -- | 0 | Yaqi Wang, Guoqin Mai, Min Zou, Haoyu Long, Yao-Qing Chen, Litao Sun, Dechao Tian, Yang Zhao, Guozhi Jiang, Zicheng Cao, Xiangjun Du. Heavy chain sequence-based classifier for the specificity of human antibodies |
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0 | -- | 0 | Bruna Moreira da Silva, Yoochan Myung, David B. Ascher, Douglas E. V. Pires. epitope3D: a machine learning method for conformational B-cell epitope prediction |
0 | -- | 0 | Bingxiang Xu, Xiaoli Li, Xiaomeng Gao, Yan Jia, Jing Liu, Feifei Li, Zhihua Zhang. DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data |
0 | -- | 0 | Mario Flores, Zhentao Liu, Tinghe Zhang, Md Musaddaqui Hasib, Yu-Chiao Chiu, Zhenqing Ye, Karla Paniagua, Sumin Jo, Jianqiu Zhang, Shou-Jiang Gao, Yu-Fang Jin, Yidong Chen, Yufei Huang. Deep learning tackles single-cell analysis - a survey of deep learning for scRNA-seq analysis |
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0 | -- | 0 | Qiaoming Liu, Jun Wan 0002, Guohua Wang. A survey on computational methods in discovering protein inhibitors of SARS-CoV-2 |
0 | -- | 0 | Fuhao Zhang, Bi Zhao, Wenbo Shi, Min Li 0007, Lukasz A. Kurgan. DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning |
0 | -- | 0 | Hui-Sheng Li, Le Ou-Yang, Yuan Zhu, Hong Yan 0001, Xiao-fei Zhang. scDEA: differential expression analysis in single-cell RNA-sequencing data via ensemble learning |
0 | -- | 0 | Kengo Sato, Yuki Kato. Prediction of RNA secondary structure including pseudoknots for long sequences |
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0 | -- | 0 | Héctor Buena Maizón, Francisco J. Barrantes. A deep learning-based approach to model anomalous diffusion of membrane proteins: the case of the nicotinic acetylcholine receptor |
0 | -- | 0 | Yi Yang, Xingjie Shi, Wei Liu, Qiuzhong Zhou, Mai Chan Lau, Jeffrey Chun Tatt Lim, Lei Sun, Cedric Chuan Young Ng, Joe Yeong, Jin Liu. SC-MEB: spatial clustering with hidden Markov random field using empirical Bayes |
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0 | -- | 0 | Umm-Kulthum Ismail Umlai, Dhinoth Kumar Bangarusamy, Xavier Estivill, Puthen Veettil Jithesh. Genome sequencing data analysis for rare disease gene discovery |
0 | -- | 0 | Bin Yang, Wenzheng Bao, Jinglong Wang. Active disease-related compound identification based on capsule network |
0 | -- | 0 | Qian Cheng, Shuqing Jiang, Feng Xu, Qian Wang, Yingjie Xiao, Ruyang Zhang, Jiuran Zhao, Jianbing Yan, Chuang Ma, Xiangfeng Wang. Genome optimization via virtual simulation to accelerate maize hybrid breeding |
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0 | -- | 0 | Cui-Xiang Lin, Hong-Dong Li, Chao Deng, Weisheng Liu, Shannon Erhardt, Fang-Xiang Wu, Xing-Ming Zhao, Yuanfang Guan, Jun Wang, Daifeng Wang, Bin Hu, Jianxin Wang. An integrated brain-specific network identifies genes associated with neuropathologic and clinical traits of Alzheimer's disease |
0 | -- | 0 | Robert Schwarz, Philipp Koch, Jeanne Wilbrandt, Steve Hoffmann. Locus-specific expression analysis of transposable elements |
0 | -- | 0 | Mengting Niu, Ying Ju, Chen Lin, Quan Zou 0001. Characterizing viral circRNAs and their application in identifying circRNAs in viruses |
0 | -- | 0 | Fangfang Xia, Jonathan E. Allen, Prasanna Balaprakash, Thomas S. Brettin, Cristina Garcia-Cardona, Austin Clyde, Judith D. Cohn, James H. Doroshow, Xiaotian Duan, Veronika Dubinkina, Yvonne A. Evrard, Ya-Ju Fan, Jason Gans, Stewart He, Pinyi Lu, Sergei Maslov, Alexander Partin, Maulik Shukla, Eric A. Stahlberg, Justin M. Wozniak, Hyun Seung Yoo, George F. Zaki, Yitan Zhu, Rick Stevens. A cross-study analysis of drug response prediction in cancer cell lines |
0 | -- | 0 | Le Ou-Yang, Fan Lu, Zi-Chao Zhang, Min Wu 0008. Matrix factorization for biomedical link prediction and scRNA-seq data imputation: an empirical survey |
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0 | -- | 0 | Yuxin Song, Li'ang Yang, Li Jiang, Zhiyu Hao, Runqing Yang, Pao Xu. Optimizing genomic control in mixed model associations with binary diseases |
0 | -- | 0 | Andrea Bommert, Thomas Welchowski, Matthias Schmid, Jörg Rahnenführer. Benchmark of filter methods for feature selection in high-dimensional gene expression survival data |
0 | -- | 0 | Jiankang Wang, Ryuichiro Nakato. HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data |
0 | -- | 0 | Wei Peng, Qi Tang, Wei Dai, Tielin Chen. Improving cancer driver gene identification using multi-task learning on graph convolutional network |
0 | -- | 0 | Shenggeng Lin, Yanjing Wang 0003, LingFeng Zhang, Yanyi Chu, Yatong Liu, Yitian Fang, Mingming Jiang, Qiankun Wang, Bowen Zhao, Yi Xiong, Dong-Qing Wei. MDF-SA-DDI: predicting drug-drug interaction events based on multi-source drug fusion, multi-source feature fusion and transformer self-attention mechanism |
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0 | -- | 0 | Fang Ge, Ying Zhang 0053, Jian Xu, Muhammad Arif, Jiangning Song, Dong-jun Yu. Prediction of disease-associated nsSNPs by integrating multi-scale ResNet models with deep feature fusion |
0 | -- | 0 | Dan Shao, Yinfei Dai, Nianfeng Li, Xuqing Cao, Wei Zhao, Li Cheng, Zhuqing Rong, Lan Huang 0002, Yan Wang 0028, Jing Zhao. Artificial intelligence in clinical research of cancers |
0 | -- | 0 | Margaret G. Guo, Daniel N. Sosa, Russ B. Altman. Challenges and opportunities in network-based solutions for biological questions |
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0 | -- | 0 | Yumeng Zhang, Yangming Zhang, Yi Xiong, Hui Wang, Zixin Deng, Jiangning Song, Hong-Yu Ou. T4SEfinder: a bioinformatics tool for genome-scale prediction of bacterial type IV secreted effectors using pre-trained protein language model |
0 | -- | 0 | Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li. Somatic variant analysis suite: copy number variation clonal visualization online platform for large-scale single-cell genomics |
0 | -- | 0 | Tiantian Liu, Peirong Xu, Yueyao Du, Hui Lu 0004, Hongyu Zhao, Tao Wang 0067. MZINBVA: variational approximation for multilevel zero-inflated negative-binomial models for association analysis in microbiome surveys |
0 | -- | 0 | Ruohan Wang, Xiang-Li-Lan Zhang, Jianping Wang, Shuai Cheng Li 0001. DeepHost: phage host prediction with convolutional neural network |
0 | -- | 0 | Hao Lv, Yang Zhang, Jia-Shu Wang, Shi-Shi Yuan, Zi-Jie Sun, Fu-Ying Dao, Zheng-Xing Guan, Hao Lin 0001, Ke-Jun Deng. iRice-MS: An integrated XGBoost model for detecting multitype post-translational modification sites in rice |
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0 | -- | 0 | Farzaneh Firoozbakht, Behnam Yousefi, Benno Schwikowski. An overview of machine learning methods for monotherapy drug response prediction |
0 | -- | 0 | Yu Sun, Haicheng Li, Lei Zheng, Jinzhao Li, Yan Hong, Pengfei Liang, Lai-Yu Kwok, Yongchun Zuo, Wenyi Zhang, Heping Zhang. iProbiotics: a machine learning platform for rapid identification of probiotic properties from whole-genome primary sequences |
0 | -- | 0 | Kevin Bu, David S. Wallach, Zach Wilson, Nan Shen, Leopoldo N. Segal, Emilia Bagiella, José Carlos Clemente. Identifying correlations driven by influential observations in large datasets |
0 | -- | 0 | Waqar Hussain. sAMP-PFPDeep: Improving accuracy of short antimicrobial peptides prediction using three different sequence encodings and deep neural networks |
0 | -- | 0 | Chuanxing Li, Jing Gao, Zicheng Zhang, Lu Chen, Xun Li, Meng Zhou 0003, Åsa M. Wheelock. Multiomics integration-based molecular characterizations of COVID-19 |
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0 | -- | 0 | Ashwin Dhakal, Cole McKay, John J. Tanner, Jianlin Cheng. Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions |
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0 | -- | 0 | Bo Zhang, Jianghua He, Jinxiang Hu, Devin C. Koestler, Prabhakar Chalise. Letter to the Editor: on the stability and internal consistency of component-wise sparse mixture regression-based clustering |
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0 | -- | 0 | Eun-Gyeong Park, Sung-Jin Pyo, Youxi Cui, Sang Ho Yoon, Jin-Wu Nam. Tumor immune microenvironment lncRNAs |
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0 | -- | 0 | Mohammad Reza Karimi, Amir-Hossein Karimi, Shamsozoha Abolmaali, Mehdi Sadeghi, Ulf Schmitz. Prospects and challenges of cancer systems medicine: from genes to disease networks |
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0 | -- | 0 | Yurui Chen, Louxin Zhang. How much can deep learning improve prediction of the responses to drugs in cancer cell lines? |
0 | -- | 0 | Huan Liu, Quan Zou, Yun Xu. A novel fast multiple nucleotide sequence alignment method based on FM-index |
0 | -- | 0 | Yuan Luo 0001. Evaluating the state of the art in missing data imputation for clinical data |
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0 | -- | 0 | Priyank Shukla, Preeti Pandey, Bodhayan Prasad, Tony Robinson, Rituraj Purohit, Leon G. D'cruz, Murtaza M. Tambuwala, Ankur Mutreja, Jim Harkin, Taranjit Singh Rai, Elaine K. Murray, David S. Gibson, Anthony J. Bjourson. Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage |
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0 | -- | 0 | Meng-Huan Song, Chaochao Yan, Jiatang Li. MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data |
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0 | -- | 0 | Ping Xuan, Mengsi Fan, Hui Cui, Tiangang Zhang, Toshiya Nakaguchi. GVDTI: graph convolutional and variational autoencoders with attribute-level attention for drug-protein interaction prediction |
0 | -- | 0 | Shaherin Basith, Gwang Lee, Balachandran Manavalan. STALLION: a stacking-based ensemble learning framework for prokaryotic lysine acetylation site prediction |
0 | -- | 0 | Ritesh Sharma, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar 0003, Sonal Saxena, Raj Kumar Singh. Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM |
0 | -- | 0 | Jingxin Dong, Mingyi Zhao, Yuansheng Liu, Yansen Su, Xiangxiang Zeng. Deep learning in retrosynthesis planning: datasets, models and tools |
0 | -- | 0 | Jen-Hao Chen, Yufeng Jane Tseng. A general optimization protocol for molecular property prediction using a deep learning network |
0 | -- | 0 | Zijun Zhu, Sainan Zhang, Ping Wang, Xinyu Chen, Jianxing Bi, Liang Cheng 0006, Xue Zhang. A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19 |
0 | -- | 0 | Zhao Chen, Yin Jiang, Xiaoyu Zhang, Rui Zheng, Ruijin Qiu, Yang Sun, Chen Zhao, Hongcai Shang. ResNet18DNN: prediction approach of drug-induced liver injury by deep neural network with ResNet18 |
0 | -- | 0 | Hui Li, Zhaohong Deng, Haitao Yang, Xiaoyong Pan, Zhisheng Wei, Hong-bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang 0001, Jing Wu. circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier |
0 | -- | 0 | Jiacheng Wang, Quan Zou, Chen Lin. A comparison of deep learning-based pre-processing and clustering approaches for single-cell RNA sequencing data |
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0 | -- | 0 | Enrico Gaffo, Alessia Buratin, Anna Dal Molin, Stefania Bortoluzzi. Sensitive, reliable and robust circRNA detection from RNA-seq with CirComPara2 |
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0 | -- | 0 | He Li, Hangxiao Zhang, Hangjin Jiang. Combining power of different methods to detect associations in large data sets |
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