| 0 | -- | 0 | Etienne Boileau, Janine Altmüller, Isabel S. Naarmann-de Vries, Christoph Dieterich. A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover |
| 0 | -- | 0 | Ritesh Sharma, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar 0003, Sonal Saxena, Raj Kumar Singh. AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom |
| 0 | -- | 0 | Pengfei Pei, Hongbo Qin, Jialin Chen, Fengli Wang, Chengzhi He, Shiting He, Bixia Hong, Ke Liu, Renzhong Qiao, Huahao Fan, Yigang Tong, Long Chen, Shi-Zhong Luo. Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein |
| 0 | -- | 0 | Forrest C. Koch, Gavin J. Sutton, Irina Voineagu, Fatemeh Vafaee. Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data |
| 0 | -- | 0 | Bowen Song, Kunqi Chen, Yujiao Tang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng. ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome |
| 0 | -- | 0 | Brian B. Nadel, Meritxell Oliva, Benjamin L. Shou, Keith Mitchell, Feiyang Ma, Dennis J. Montoya, Alice Mouton, Sarah Kim-Hellmuth, Barbara E. Stranger, Matteo Pellegrini, Serghei Mangul. Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples |
| 0 | -- | 0 | Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence Ettwiller, Qin Ma, Bingqiang Liu. A novel computational framework for genome-scale alternative transcription units prediction |
| 0 | -- | 0 | Patrick Brendan Timmons, Chandralal M. Hewage. ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides |
| 0 | -- | 0 | Yumei Li, Qing Sunny Shen, Qi Peng, Wanqiu Ding, Jie Zhang, Xiaoming Zhong, Ni A. An, Mingjun Ji, Wei-Zhen Zhou, Chuan-Yun Li. Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure |
| 0 | -- | 0 | Chunmei Cui, Yuan Zhou, Qinghua Cui. Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation |
| 0 | -- | 0 | Yunda Si, Chengfei Yan. Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function |
| 0 | -- | 0 | Deborah F. Nacer, Helena Liljedahl, Anna Karlsson, David Lindgren, Johan Staaf. Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor |
| 0 | -- | 0 | Xuan Xiao, Yu-Tao Shao, Xiang Cheng, Biljana Stamatovic. iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for identifying antimicrobial peptides and their functional types |
| 0 | -- | 0 | Peilin Jia, Astrid Marilyn Manuel, Brisa S. Fernandes, Yulin Dai, Zhongming Zhao. Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity |
| 0 | -- | 0 | Congting Ye, Danhui Zhao, Wenbin Ye 0002, Xiaohui Wu, Guoli Ji, Qingshun Quinn Li, Juncheng Lin. QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering |
| 0 | -- | 0 | Yue Zhang, Jianyuan Lin, Lianmin Zhao, Xiangxiang Zeng, Xiangrong Liu. A novel antibacterial peptide recognition algorithm based on BERT |
| 0 | -- | 0 | Zulkar Nain, Shital K. Barman, Md Moinuddin Sheam, Shifath Bin Syed, Abdus Samad, Julian M. W. Quinn, Mohammad Minnatul Karim, Mahbubul Kabir Himel, Rajib Kanti Roy, Mohammad Ali Moni, Sudhangshu Kumar Biswas. Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions |
| 0 | -- | 0 | Angelo Fortunato, Diego Mallo, Shawn M. Rupp, Lorraine M. King, Timothy Hardman, Joseph Y. Lo, Allison Hall, Jeffrey R. Marks, E. Shelley Hwang, Carlo C. Maley. A new method to accurately identify single nucleotide variants using small FFPE breast samples |
| 0 | -- | 0 | Bosheng Song, Fen Li, Yuansheng Liu, Xiangxiang Zeng. Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison |
| 0 | -- | 0 | Amarinder Singh Thind, Isha Monga, Prasoon Kumar Thakur, Pallawi Kumari, Kiran Dindhoria, Monika Krzak, Marie Ranson, Bruce Ashford. Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology |
| 0 | -- | 0 | Bethan Yates, Kristian A. Gray, Tamsin E. M. Jones, Elspeth A. Bruford. Updates to HCOP: the HGNC comparison of orthology predictions tool |
| 0 | -- | 0 | Ying Zhang 0053, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-jun Yu. Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites |
| 0 | -- | 0 | Phasit Charoenkwan, Wararat Chiangjong, Chanin Nantasenamat, Md Mehedi Hasan, Balachandran Manavalan, Watshara Shoombuatong. StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides |
| 0 | -- | 0 | Anna Onisiforou, George M. Spyrou. Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches |
| 0 | -- | 0 | Xingjian Chen, Lingjing Liu, Weitong Zhang, Jianyi Yang, Ka Chun Wong. Human host status inference from temporal microbiome changes via recurrent neural networks |
| 0 | -- | 0 | Fengqing Lu, Mufei Li, Xiaoping Min, Chunyan Li, Xiangxiang Zeng. De novo generation of dual-target ligands using adversarial training and reinforcement learning |
| 0 | -- | 0 | Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I Webb, Jiangning Song. Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations |
| 0 | -- | 0 | Bulat Zagidullin, Ziyan Wang, Yuanfang Guan, Esa Pitkänen, Jing Tang 0002. Comparative analysis of molecular fingerprints in prediction of drug combination effects |
| 0 | -- | 0 | Bingxing An, Mang Liang, Tianpeng Chang, Xinghai Duan, Lili Du, Lingyang Xu, Lupei Zhang, Xue Gao, Junya Li, Huijiang Gao. KCRR: a nonlinear machine learning with a modified genomic similarity matrix improved the genomic prediction efficiency |
| 0 | -- | 0 | Zhiyu Hao, Jin Gao, Yuxin Song, Runqing Yang, Di Liu. Genome-wide hierarchical mixed model association analysis |
| 0 | -- | 0 | Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill L. Wegrzyn, Tavis Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily S. Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter 0001, Joe West, Stephen P. Ficklin. Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases |
| 0 | -- | 0 | Le Ou-Yang, Dehan Cai, Xiao-fei Zhang, Hong Yan 0001. WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values |
| 0 | -- | 0 | Yan Li, Shao-Wu Zhang. Resilience function uncovers the critical transitions in cancer initiation |
| 0 | -- | 0 | Hao Lv, Lei Shi, Joshua William Berkenpas, Fu-Ying Dao, Hasan Zulfiqar, Hui Ding 0005, Yang Zhang, Liming Yang, Renzhi Cao. Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design |
| 0 | -- | 0 | Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin. Porpoise: a new approach for accurate prediction of RNA pseudouridine sites |
| 0 | -- | 0 | Anson T. Ku, Scott Wilkinson, Adam G. Sowalsky. Comparison of approaches to transcriptomic analysis in multi-sampled tumors |
| 0 | -- | 0 | Marios Tomazou, Marilena M. Bourdakou, George Minadakis, Margarita Zachariou, Anastasis Oulas, Evangelos Karatzas, Eleni M. Loizidou, Andrea C. Kakouri, Christiana C. Christodoulou, Kyriaki Savva, Maria Zanti, Anna Onisiforou, Sotiroula Afxenti, Jan Richter, Christina G. Christodoulou, Theodoros Kyprianou, George Kolios, Nikolas Dietis, George M. Spyrou. Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19 |
| 0 | -- | 0 | Valentina Galata, Susheel Bhanu Busi, Benoît Josef Kunath, Laura de Nies, Magdalena Calusinska, Rashi Halder, Patrick May, Paul Wilmes, Cedric Christian Laczny. Functional meta-omics provide critical insights into long- and short-read assemblies |
| 0 | -- | 0 | Subhayan Chattopadhyay, Jenny Karlsson, Anders Valind, Natalie Andersson, David Gisselsson. Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST |
| 0 | -- | 0 | Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-bin Shen. Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network |
| 0 | -- | 0 | Yu Cheng, Yongshun Gong, Yuansheng Liu, Bosheng Song, Quan Zou. Molecular design in drug discovery: a comprehensive review of deep generative models |
| 0 | -- | 0 | Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang. scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species |
| 0 | -- | 0 | Shaherin Basith, Md. Mehedi Hasan 0002, Gwang Lee, Leyi Wei, Balachandran Manavalan. Integrative machine learning framework for the identification of cell-specific enhancers from the human genome |
| 0 | -- | 0 | Meng Zou, Zhana Duren, Qiuyue Yuan, Henry Li, Andrew Paul Hutchins, Wing Hung Wong, Yong Wang. MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting |
| 0 | -- | 0 | Ai Ni, Li-Xuan Qin. Performance evaluation of transcriptomics data normalization for survival risk prediction |
| 0 | -- | 0 | Shuquan Rao, Ancha Baranova, Hongbao Cao, Jiu Chen, Xiangrong Zhang, Fuquan Zhang. Corrigendum to: Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption |
| 0 | -- | 0 | Xinru Tang, Jiawei Luo, Cong Shen, Zihan Lai. Multi-view Multichannel Attention Graph Convolutional Network for miRNA-disease association prediction |
| 0 | -- | 0 | Hansi Zheng, Amlan Talukder, Xiaoman Li, Haiyan Hu. A systematic evaluation of the computational tools for lncRNA identification |
| 0 | -- | 0 | Yushan Qiu, Wai-Ki Ching, Quan Zou 0001. Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transition |
| 0 | -- | 0 | Ronald Yurko, Kathryn Roeder, Bernie Devlin, Max G'Sell. An approach to gene-based testing accounting for dependence of tests among nearby genes |
| 0 | -- | 0 | Jiajun Yang, Dongyang Wang, Yanbo Yang, Wenqian Yang, Weiwei Jin, Xiaohui Niu, Jing Gong. A systematic comparison of normalization methods for eQTL analysis |
| 0 | -- | 0 | Xin Chen, Wei Gao, Jie Li, Dongfang You, Zhaolei Yu, Mingzhi Zhang, Fang Shao, Yongyue Wei, Ruyang Zhang, Theis Lange, Qianghu Wang, Feng Chen, Xiang Lu, Yang Zhao. A predictive paradigm for COVID-19 prognosis based on the longitudinal measure of biomarkers |
| 0 | -- | 0 | Leiv Rønneberg, Andrea Cremaschi, Robert Hanes, Jorrit M. Enserink, Manuela Zucknick. bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments |
| 0 | -- | 0 | Qiu Xiao, Yu Fu, Yide Yang, Jianhua Dai, Jiawei Luo. NSL2CD: identifying potential circRNA-disease associations based on network embedding and subspace learning |
| 0 | -- | 0 | Alok Sharma, Artem Lysenko, Keith A. Boroevich, Edwin Vans, Tatsuhiko Tsunoda. DeepFeature: feature selection in nonimage data using convolutional neural network |
| 0 | -- | 0 | Thomas Gaudelet, Ben Day, Arian R. Jamasb, Jyothish Soman, Cristian Regep, Gertrude Liu, Jeremy B. R. Hayter, Richard Vickers, Charles Roberts, Jian Tang, David Roblin, Tom L. Blundell, Michael M. Bronstein, Jake P. Taylor-King. Utilizing graph machine learning within drug discovery and development |
| 0 | -- | 0 | Jian Chen, Xiaojun Qian, Yifu He, Xinghua Han, Yueyin Pan. An artificial neural network model based on DNA damage response genes to predict outcomes of lower-grade glioma patients |
| 0 | -- | 0 | Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-jun Yu. Improving protein fold recognition using triplet network and ensemble deep learning |
| 0 | -- | 0 | Kath Nicholls, Chris Wallace. Comparison of sparse biclustering algorithms for gene expression datasets |
| 0 | -- | 0 | Wenlong Jia, Chang Xu, Shuai Cheng Li 0001. Resolving complex structures at oncovirus integration loci with conjugate graph |
| 0 | -- | 0 | Md. Mehedi Hasan 0002, Md. Ashad Alam, Watshara Shoombuatong, Hong-Wen Deng, Balachandran Manavalan, Hiroyuki Kurata. NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning |
| 0 | -- | 0 | Kexin Chen, Haoming Xu, Yiming Lei, Pietro Lió, Yuan Li, Hongyan Guo, Mohammad Ali Moni. Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance |
| 0 | -- | 0 | Mingming Jiang, Bowen Zhao, Shenggan Luo, Qiankun Wang, Yanyi Chu, Tianhang Chen, Xueying Mao, Yatong Liu, Yanjing Wang 0003, Xue Jiang, Dong-Qing Wei, Yi Xiong. NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods |
| 0 | -- | 0 | Maria Bernard, Olivier Rué, Mahendra Mariadassou, Géraldine Pascal. FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers |
| 0 | -- | 0 | Ye Wang, Yuchao Jiang, Bing Yao, Kun Huang, Yunlong Liu, Yue Wang, Xiao Qin 0001, Andrew J. Saykin, Li Chen. WEVar: a novel statistical learning framework for predicting noncoding regulatory variants |
| 0 | -- | 0 | Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang. Distance-guided protein folding based on generalized descent direction |
| 0 | -- | 0 | Vishakha Gautam, Aayushi Mittal, Siddhant Kalra, Sanjay Kumar Mohanty, Krishan Gupta, Komal Rani, Srivatsava Naidu, Tripti Mishra, Debarka Sengupta, Gaurav Ahuja. EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies |
| 0 | -- | 0 | Limin Jiang, Hui Yu, Jiawei Li, Jijun Tang, Yan Guo, Fei Guo. Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution |
| 0 | -- | 0 | Chi-Chi Zhu, Chun-Chun Wang, Yan Zhao, Mingcheng Zuo, Xing Chen 0001. Identification of miRNA-disease associations via multiple information integration with Bayesian ranking |
| 0 | -- | 0 | Chenxing Zhang, Lin Gao 0006, Bingbo Wang, Yong Gao. Improving Single-Cell RNA-seq Clustering by Integrating Pathways |
| 0 | -- | 0 | Kewalin Samart, Phoebe Tuyishime, Arjun Krishnan, Janani Ravi. Reconciling multiple connectivity scores for drug repurposing |
| 0 | -- | 0 | Cheng-Kun Wu, Xiao-Chen Zhang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao 0001. Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules |
| 0 | -- | 0 | Shuo Shi, Qiheng Qian, Shuhuan Yu, Qi Wang, Jinyue Wang, Jingyao Zeng, Zhenglin Du, Jing-Fa Xiao. RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks |
| 0 | -- | 0 | Sagnik Sen 0002, Ashmita Dey, Sanghamitra Bandhyopadhyay, Vladimir N. Uversky, Ujjwal Maulik. Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities |
| 0 | -- | 0 | Chun-Chun Wang, Chen-Di Han, Qi Zhao, Xing Chen. Circular RNAs and complex diseases: from experimental results to computational models |
| 0 | -- | 0 | Mauro de Medeiros Oliveira, Ígor Bonadio, Alicia Lie de Melo, Glaucia Mendes Souza, Alan Mitchell Durham. TSSFinder - fast and accurate ab initio prediction of the core promoter in eukaryotic genomes |
| 0 | -- | 0 | Jing Qin 0004, Yaohua Hu, Jen-Chih Yao, Ricky Wai Tak Leung, Yongqiang Zhou, Yiming Qin, Junwen Wang. Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data |
| 0 | -- | 0 | Pengyong Li, Jun Wang, Yixuan Qiao, Hao Chen, Yihuan Yu, Xiaojun Yao, Peng Gao, Guotong Xie, Sen Song. An effective self-supervised framework for learning expressive molecular global representations to drug discovery |
| 0 | -- | 0 | Carlos A. Ortiz-Mahecha, William A. Agudelo, Manuel A. Patarroyo, Manuel-Elkin Patarroyo, Carlos F. Suárez. MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models |
| 0 | -- | 0 | Yuxuan Pang, Lantian Yao, Jhih-Hua Jhong, Zhuo Wang, Tzong-Yi Lee. AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches |
| 0 | -- | 0 | Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-jun Yu. PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection |
| 0 | -- | 0 | Linhui Xie, Bing He, Pradeep Varathan, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Paul Salama, Jingwen Yan. Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease |
| 0 | -- | 0 | Shuhui Liu, Yupei Zhang, Xuequn Shang, Zhaolei Zhang. ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes |
| 0 | -- | 0 | Qi An, Liang Yu. A heterogeneous network embedding framework for predicting similarity-based drug-target interactions |
| 0 | -- | 0 | Haluk Dogan, Zeynep Hakguder, Roland Madadjim, Stephen Scott 0001, Massimiliano Pierobon, Juan Cui. Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning |
| 0 | -- | 0 | Yuzhao Zhang, Xibing He, Jingchen Zhai, Beihong Ji, Viet Hoang Man, Junmei Wang. In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor |
| 0 | -- | 0 | Seyoon Ko, Ginny X. Li, Hyungwon Choi, Joong-Ho Won. Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx |
| 0 | -- | 0 | Bingbo Wang, Xianan Dong, Jie Hu, Xiujuan Ma, Chao Han, Yajun Wang, Lin Gao 0006. The peripheral and core regions of virus-host network of COVID-19 |
| 0 | -- | 0 | Khandakar Tanvir Ahmed, Jiao Sun, William Chen, Irene Martinez, Sze Cheng, Wencai Zhang, Jeongsik Yong, Wei Zhang 0076. In silico model for miRNA-mediated regulatory network in cancer |
| 0 | -- | 0 | Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard. Deep learning-based real-time detection of novel pathogens during sequencing |
| 0 | -- | 0 | Xiaoqi Wang, Bin Xin, Weihong Tan, Zhijian Xu, Kenli Li 0001, Fei Li, Wu Zhong, Shaoliang Peng. DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19 |
| 0 | -- | 0 | Yang Yang, Timothy M. Walker, Samaneh Kouchaki, Chenyang Wang, Timothy E. A Peto, Derrick W. Crook, David A. Clifton. An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction |
| 0 | -- | 0 | Qiujie Lv, Guanxing Chen, Lu Zhao, Weihe Zhong, Calvin Yu-Chian Chen. Mol2Context-vec: learning molecular representation from context awareness for drug discovery |
| 0 | -- | 0 | Yichen Guo, Ke Yan 0003, Hongwu Lv, Bin Liu. PreTP-EL: prediction of therapeutic peptides based on ensemble learning |
| 0 | -- | 0 | Zhaochun Xu, Meng Luo, Weizhong Lin, Guangfu Xue, Pingping Wang, Xiyun Jin, Chang Xu, Wenyang Zhou, Yideng Cai, Wenyi Yang, Huan Nie, Qinghua Jiang. DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor |
| 0 | -- | 0 | Hilal Tayara, Ibrahim Abdelbaky, Kil To Chong. Recent omics-based computational methods for COVID-19 drug discovery and repurposing |
| 0 | -- | 0 | Janak Sunuwar, Rajeev K. Azad. A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains |
| 0 | -- | 0 | Haochen Zhao, Kai Zheng, Yaohang Li, Jianxin Wang. A novel graph attention model for predicting frequencies of drug-side effects from multi-view data |
| 0 | -- | 0 | Tyrone Chen, Melcy Philip, Kim-Anh Lê Cao, Sonika Tyagi. A multi-modal data harmonisation approach for discovery of COVID-19 drug targets |
| 0 | -- | 0 | Wei Zhang, Qiaozhen Meng, Jijun Tang, Fei Guo. Exploring effectiveness of ab-initio protein-protein docking methods on a novel antibacterial protein complex dataset |
| 0 | -- | 0 | Sho Tsukiyama, Md. Mehedi Hasan 0002, Satoshi Fujii, Hiroyuki Kurata. LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec |
| 0 | -- | 0 | Raghvendra Mall, Mohamad Saad 0001, Jessica Roelands, Darawan Rinchai, Khalid Kunji, Hossam Almeer, Wouter Hendrickx, Francesco M. Marincola, Michele Ceccarelli, Davide Bedognetti. Network-based identification of key master regulators associated with an immune-silent cancer phenotype |
| 0 | -- | 0 | Luyao Qin, Xiao Ding, Yongjie Li, Qingfeng Chen, Jing Meng, Taijiao Jiang. Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2 |
| 0 | -- | 0 | Zhenla Jiang, Jianrong Xu, Aixia Yan, Ling Wang 0008. A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening |
| 0 | -- | 0 | Yin Jin, Zheng Wang, An-Yu Dong, Yuan-Qin Huang, Ge-Fei Hao, Bao-An Song. Web repositories of natural agents promote pests and pathogenic microbes management |
| 0 | -- | 0 | Jing-Yi Li, Shen Jin, Xin-Ming Tu, Yang Ding, Ge Gao. Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network |
| 0 | -- | 0 | Haocheng Ding, Lingsong Meng, Andrew C. Liu, Michelle L. Gumz, Andrew J. Bryant, Colleen A. Mcclung, George C. Tseng, Karyn A. Esser, Zhiguang Huo. Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications |
| 0 | -- | 0 | Fei Qin, Xizhi Luo, Guoshuai Cai, Feifei Xiao. Shall genomic correlation structure be considered in copy number variants detection? |
| 0 | -- | 0 | Funmilayo L. Makinde, Milaine S. S. Tchamga, James Jafali, Segun Fatumo, Emile R. Chimusa, Nicola Mulder, Gaston K. Mazandu. Reviewing and assessing existing meta-analysis models and tools |
| 0 | -- | 0 | Trinh-Trung-Duong Nguyen, Duc-Khanh Nguyen, Yu-Yen Ou. Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network |
| 0 | -- | 0 | Jiaxing Chen, Chinwang Cheong, Liang Lan, Xin Zhou, Jiming Liu 0001, Aiping Lyu, William K. Cheung, Lu Zhang. DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data |
| 0 | -- | 0 | Jialong Liang, Kun Zhang, Jie Yang, Xianfeng Li, Qinglan Li, Yan Wang, Wanshi Cai, Huajing Teng, Zhongsheng Sun. A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing |
| 0 | -- | 0 | Pengfei Liang, Lei Zheng, Chunshen Long, Wuritu Yang, Lei Yang, Yongchun Zuo. HelPredictor models single-cell transcriptome to predict human embryo lineage allocation |
| 0 | -- | 0 | Lijun Cai, Changcheng Lu, Junlin Xu, Yajie Meng, Peng Wang, Xiangzheng Fu, Xiangxiang Zeng, Yansen Su. Drug repositioning based on the heterogeneous information fusion graph convolutional network |
| 0 | -- | 0 | Betül Güvenç Paltun, Samuel Kaski, Hiroshi Mamitsuka. Machine learning approaches for drug combination therapies |
| 0 | -- | 0 | Gerald van Eeden, Caitlin Uren, Gian van der Spuy, Gerard Tromp, Marlo Möller. Local ancestry inference in heterogeneous populations - Are recent recombination events more relevant? |
| 0 | -- | 0 | Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone C. Castellani, Luciano Milanesi, Daniel Remondini. Characterization and comparison of gene-centered human interactomes |
| 0 | -- | 0 | Chen Lyu, Manyan Huang, Nianjun Liu, Zhongxue Chen, Philip J. Lupo, Benjamin Tycko, John S. Witte, Charlotte A. Hobbs, Ming Li. Detecting methylation quantitative trait loci using a methylation random field method |
| 0 | -- | 0 | Chayanit Piyawajanusorn, Linh C. Nguyen, Ghita Ghislat, Pedro J. Ballester. A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling |
| 0 | -- | 0 | Xiao-Chen Zhang, Cheng-Kun Wu, Zhi-Jiang Yang, Zhen-Xing Wu, Jia-Cai Yi, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao 0001. MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction |
| 0 | -- | 0 | Teemu J. Rintala, Antonio Federico, Leena Latonen, Dario Greco, Vittorio Fortino. A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery |
| 0 | -- | 0 | Aman Chandra Kaushik, Qiqi Wu, Li Lin, Haibo Li, Longqi Zhao, Zilu Wen, Yanzheng Song, Qihang Wu, Jin Wang, Xiaokui Guo, Hualin Wang, Xiaoli Yu, Dongqing Wei, Shulin Zhang. Exosomal ncRNAs profiling of mycobacterial infection identified miRNA-185-5p as a novel biomarker for tuberculosis |
| 0 | -- | 0 | Yu Zhang 0084, Yichao Cai, Xavier Roca, Chee-Keong Kwoh 0001, Melissa Jane Fullwood. Chromatin loop anchors predict transcript and exon usage |
| 0 | -- | 0 | Tamar Sofer, Nuzulul Kurniansyah, François Aguet, Kristin G. Ardlie, Peter Durda, Deborah A. Nickerson, Joshua D. Smith, Yongmei Liu, Sina Gharib, Susan Redline, Stephen S. Rich, Jerome I. Rotter, Kent D. Taylor. Benchmarking association analyses of continuous exposures with RNA-seq in observational studies |
| 0 | -- | 0 | Ali F. Alsulami, Pedro H. M. Torres, Ismail Moghul, Sheikh Mohammed Arif, Amanda K. Chaplin, Sundeep Chaitanya Vedithi, Tom L. Blundell. COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets |
| 0 | -- | 0 | Wenying He, Jijun Tang, Quan Zou 0001, Fei Guo. MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction |
| 0 | -- | 0 | Ruihan Luo, Chuang Ge, Xiao Xiao, Jing Song, Shiqi Miao, Yongyao Tang, Jiayi Lai, Weiqi Nian, Fangzhou Song, Longke Ran. Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment |
| 0 | -- | 0 | Bonil Koo, Je-Keun Rhee. Prediction of tumor purity from gene expression data using machine learning |
| 0 | -- | 0 | Xing Chen, Chi Zhou, Chun-Chun Wang, Yan Zhao. Predicting potential small molecule-miRNA associations based on bounded nuclear norm regularization |
| 0 | -- | 0 | Yanqiang Han, Zhilong Wang, Zhiyun Wei, Jinyun Liu, Jinjin Li. Machine learning builds full-QM precision protein force fields in seconds |
| 0 | -- | 0 | R. Prabakaran, Puneet Rawat, Sandeep Kumar, M. Michael Gromiha. Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets |
| 0 | -- | 0 | Philip Davies, Matt Jones 0006, Juntai Liu, Daniel Hebenstreit. Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision |
| 0 | -- | 0 | Dalwinder Singh, Akansha Madhawan, Joy Roy. Erratum to: Identification of multiple RNAs using feature fusion |
| 0 | -- | 0 | Ruiqi Lyu, Jianle Sun, Dong Xu, Qianxue Jiang, Chaochun Wei, Yue Zhang. GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes |
| 0 | -- | 0 | Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song. nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning |
| 0 | -- | 0 | Aleksandra A. Galitsyna, Mikhail S. Gelfand. Single-cell Hi-C data analysis: safety in numbers |
| 0 | -- | 0 | Yongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou 0001. High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method |
| 0 | -- | 0 | Nikhita Gogate, Daniel Lyman, Amanda Bell, Edmund Cauley, Keith A. Crandall, Ashia Joseph, Robel Y. Kahsay, Darren A. Natale, Lynn M. Schriml, Sabyasach Sen, Raja Mazumder. COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model |
| 0 | -- | 0 | Jingzhe Lu, Xu Wang, Keyong Sun, Xun Lan. Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data |
| 0 | -- | 0 | Shiwei Wang, Qi Sun, Youjun Xu, Jianfeng Pei, Luhua Lai. A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2 |
| 0 | -- | 0 | Md Asif Nashiry, Shauli Sarmin Sumi, Mohammad Umer Sharif Shohan, Salem A. Alyami, A. K. M. Azad, Mohammad Ali Moni. Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders |
| 0 | -- | 0 | Limin Jiang, Yan Guo, Hui Yu, Kendal Hoff, Xun Ding, Wei Zhou, Jeremy Edwards. Detecting SARS-CoV-2 and its variant strains with a full genome tiling array |
| 0 | -- | 0 | Florian Borchert, Andreas Mock, Aurelie Tomczak, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P. Schapranow. Knowledge bases and software support for variant interpretation in precision oncology |
| 0 | -- | 0 | Lu Liu, Xikang Feng, Haimei Li, Shuai Cheng Li, Qiujin Qian, Yufeng Wang. Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5 |
| 0 | -- | 0 | Yongzhuang Liu, Xiaoliang Wu, Yadong Wang. An integrated approach for copy number variation discovery in parent-offspring trios |
| 0 | -- | 0 | Shokouh Rezaei, Yahya Sefidbakht, Vuk Uskokovic. Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design |
| 0 | -- | 0 | Arnold K. Nyamabo, Hui Yu, Jian-Yu Shi. SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction |
| 0 | -- | 0 | Eitamar Tripto, Yaron Orenstein. A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data |
| 0 | -- | 0 | Wenjiang Zheng, Hui Wu, Ting Wang, Shaofeng Zhan, Xiaohong Liu. Quercetin for COVID-19 and DENGUE co-infection: a potential therapeutic strategy of targeting critical host signal pathways triggered by SARS-CoV-2 and DENV |
| 0 | -- | 0 | Yaxuan Cui, Shaoqiang Zhang, Ying Liang, Xiangyun Wang, Thomas N. Ferraro, Yong Chen. Consensus clustering of single-cell RNA-seq data by enhancing network affinity |
| 0 | -- | 0 | Wei Wang, Wei Liu. PCLasso: a protein complex-based, group lasso-Cox model for accurate prognosis and risk protein complex discovery |
| 0 | -- | 0 | Zhengfeng Wang, Xiujuan Lei. Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture |
| 0 | -- | 0 | Xuan Liu, Wenbo Chen, Yu Fang, Siqi Yang, Liuping Chang, Xingyu Chen, Haidong Ye, Xinyu Tang, Shan Zhong, Wen Zhang, Zhiqiang Dong, Leng Han, Chunjiang He. ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues |
| 0 | -- | 0 | Furong Tang, Lichao Zhang, Lei Xu, Quan Zou, Hailin Feng. The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis |
| 0 | -- | 0 | Jing Xing, Shreya Paithankar, Ke Liu, Katie Uhl, Xiaopeng Li, Meehyun Ko, Seungtaek Kim, Jeremy Haskins, Bin Chen. Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals |
| 0 | -- | 0 | Lu Huo, Jiao Jiao Li, Ling Chen, Zuguo Yu, Gyorgy Hutvagner, Jinyan Li. Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects |
| 0 | -- | 0 | Hideki Yamaguchi, Yutaka Saito. Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins |
| 0 | -- | 0 | Satyajit Mahapatra, Sitanshu Sekhar Sahu. Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines |
| 0 | -- | 0 | Xi Tang, Tao Zhang, Na Cheng, Huadong Wang, Chun-Hou Zheng, Junfeng Xia, Tiejun Zhang. Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme |
| 0 | -- | 0 | Hideki Yamaguchi, Yutaka Saito. Erratum to: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins |
| 0 | -- | 0 | Kunjie Fan, Lijun Cheng, Lang Li. Artificial intelligence and machine learning methods in predicting anti-cancer drug combination effects |
| 0 | -- | 0 | Pedro H. M. Torres, Artur D. Rossi, Tom L. Blundell. ProtCHOIR: a tool for proteome-scale generation of homo-oligomers |
| 0 | -- | 0 | Jiaqi Li, Lei Wei, Xianglin Zhang, Wei Zhang, Haochen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang. DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads |
| 0 | -- | 0 | E. Sacristán-Horcajada, S. González-de la Fuente, R. Peiró-Pastor, F. Carrasco-Ramiro, R. Amils, J. M. Requena, J. Berenguer, B. Aguado. ARAMIS: From systematic errors of NGS long reads to accurate assemblies |
| 0 | -- | 0 | Hongjian Li, Gang Lu, Kam-Heung Sze, Xianwei Su, Wai-Yee Chan, Kwong-Sak Leung. Machine-learning scoring functions trained on complexes dissimilar to the test set already outperform classical counterparts on a blind benchmark |
| 0 | -- | 0 | Lin Li, Canping Chen, Xiaosheng Wang. DITHER: an algorithm for Defining IntraTumor Heterogeneity based on EntRopy |
| 0 | -- | 0 | Jie Sheng, Wei Vivian Li. Selecting gene features for unsupervised analysis of single-cell gene expression data |
| 0 | -- | 0 | Yile Huang, Yulong Qiao, Yu Zhao, Yuying Li, Jie Yuan, Jiajian Zhou, Hao Sun 0001, Huating Wang. Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms |
| 0 | -- | 0 | Xiting Wang, Meng Liu, Yiling Zhang, Shuangshuang He, Caimeng Qin, Yu Li, Tao Lu. Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery |
| 0 | -- | 0 | Stefano Castellana, Tommaso Biagini, Luca Parca, Francesco Petrizzelli, Salvatore Daniele Bianco, Angelo Luigi Vescovi, Massimo Carella, Tommaso Mazza. A comparative benchmark of classic DNA motif discovery tools on synthetic data |
| 0 | -- | 0 | Gunnar Völkel, Simon Laban, Axel Fürstberger, Silke D. Kühlwein, Nensi Ikonomi, Thomas K. Hoffmann, Cornelia Brunner, Donna S. Neuberg, Verena Gaidzik, Hartmut Döhner, Johann M. Kraus, Hans A. Kestler. Erratum to: Analysis, identification and visualization of subgroups in genomics |
| 0 | -- | 0 | Yue Zhao, Xiang-Gui Wang, Zhong-Ye Ma, Guo-Li Xiong, Zhi-Jiang Yang, Yan Cheng, Ai-Ping Lu, Zhi-jun Huang, Dong-Sheng Cao 0001. Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors |
| 0 | -- | 0 | Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang 0002, Krister Wennerberg, Tero Aittokallio. Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer |
| 0 | -- | 0 | Yixuan Huang, Peng Zhang 0050. Corrigendum to: Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data |
| 0 | -- | 0 | Miklos Diossy, Zsofia Sztupinszki, Marcin Krzystanek, Judit Borcsok, Aron C. Eklund, István Csabai, Anders Gorm Pedersen, Zoltan Szallasi. Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts |
| 0 | -- | 0 | Eloise Withnell, Xiaoyu Zhang, Kai Sun 0005, Yike Guo. XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data |
| 0 | -- | 0 | Qian Gao, Yu Zhang, Jie Liang, Hongwei Sun, Tong Wang. High-dimensional generalized propensity score with application to omics data |
| 0 | -- | 0 | Zhiqiang Yan, Jianting An, Yong Peng, Siming Kong, Qiang Liu, Ming Yang, Qilong He, Shi Song, Yidong Chen, Wei Chen, Rong Li, Jie Qiao, Liying Yan. DevOmics: an integrated multi-omics database of human and mouse early embryo |
| 0 | -- | 0 | Hongchao Liu, Huihui Yin, Guangyu Li, Junling Li, Xiaoyue Wang. Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA |
| 0 | -- | 0 | Aditya K. Padhi, Ashutosh Kumar 0001, Ken-ichi Haruna, Haruna Sato, Hiroko Tamura, Satoru Nagatoishi, Kouhei Tsumoto, Atushi Yamaguchi, Fumie Iraha, Mihoko Takahashi, Kensaku Sakamoto, Kam Y. J. Zhang. An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes |
| 0 | -- | 0 | Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang 0003, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei. MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph |
| 0 | -- | 0 | Hossein Sharifi Noghabi, Soheil Jahangiri-Tazehkand, Petr Smirnov, Casey Hon, Anthony Mammoliti, Sisira Kadambat Nair, Arvind Singh Mer, Martin Ester, Benjamin Haibe-Kains. Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models |
| 0 | -- | 0 | Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas S. Brettin, Emily M. Dietrich, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Gordon D. Pusch, Maulik Shukla, Rick Stevens, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Hyun Seung Yoo, James J. Davis 0002. A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes |
| 0 | -- | 0 | Zhi-Kai Yang, Lingyu Pan, YanMing Zhang, Hao Luo 0002, Feng Gao 0001. Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data |
| 0 | -- | 0 | Dandan Lu, Yue Zhang, Ling Zhang, Haiyan Wang, Wanlin Weng, Li Li, Hongmin Cai. Methods of privacy-preserving genomic sequencing data alignments |
| 0 | -- | 0 | Fan Hu, Lei Wang, Yishen Hu, Dongqi Wang, Weijie Wang, Jianbing Jiang, Nan Li, Peng Yin. A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe |
| 0 | -- | 0 | Danielle Maeser, Robert F. Gruener, Rong Stephanie Huang. oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data |
| 0 | -- | 0 | Serena Dotolo, Anna Marabotti, Anna Maria Rachiglio, Riziero Esposito Abate, Marco Benedetto, Fortunato Ciardiello, Antonella De Luca, Nicola Normanno, Angelo M. Facchiano, Roberto Tagliaferri. A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine |
| 0 | -- | 0 | Pengfei Pei, Hongbo Qin, Jialin Chen, Fengli Wang, Chengzhi He, Shiting He, Bixia Hong, Ke Liu, Renzhong Qiao, Huahao Fan, Yigang Tong, Long Chen, Shi-Zhong Luo. Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein |
| 0 | -- | 0 | Dalwinder Singh, Akansha Madhawan, Joy Roy. Identification of multiple RNAs using feature fusion |
| 0 | -- | 0 | Zilong Hou, Yuning Yang, Hui Li, Ka Chun Wong, Xiangtao Li. iDeepSubMito: identification of protein submitochondrial localization with deep learning |
| 0 | -- | 0 | Zhao-Yu Fang, Cui-Xiang Lin, Yun-Pei Xu, Hong-Dong Li, Qing-Song Xu. REBET: a method to determine the number of cell clusters based on batch effect removal |
| 0 | -- | 0 | Thomas Haschka, Jean Baptiste Morlot, Leopold Carron, Julien Mozziconacci. Improving distance measures between genomic tracks with mutual proximity |
| 0 | -- | 0 | Cheng-Peng Gui, Jin-Huan Wei, Yu-hang Chen, Liang-Min Fu, Yi-Ming Tang, Jia-Zheng Cao, Wei Chen, Jun-Hang Luo. A new thinking: extended application of genomic selection to screen multiomics data for development of novel hypoxia-immune biomarkers and target therapy of clear cell renal cell carcinoma |
| 0 | -- | 0 | Jiahua He, Sheng-You Huang. EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps |
| 0 | -- | 0 | Xiyun Jin, Wenyang Zhou, Meng Luo, Pingping Wang, Zhaochun Xu, Kexin Ma, Huimin Cao, Chang Xu, Yan Huang, Rui Cheng, Lixing Xiao, Xiaoyu Lin, Fenglan Pang, Yiqun Li, Huan Nie, Qinghua Jiang. Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing |
| 0 | -- | 0 | Nam Nhut Phan, Amrita Chattopadhyay, Tsui-Ting Lee, Hsiang-I Yin, Tzu-Pin Lu, Liang-Chuan Lai, Hsiao-Lin Hwa, Mong-Hsun Tsai, Eric Y. Chuang. High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data |
| 0 | -- | 0 | Yan Liu, Yuzhao Gao, Ruiling Fang, Hongyan Cao, Jian Sa, Jianrong Wang, Hongqi Liu, Tong Wang, Yuehua Cui. Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach |
| 0 | -- | 0 | Nabil Ibtehaz, Ishtiaque Ahmed, Md Sabbir Ahmed, M. Sohel Rahman, Rajeev K. Azad, Md. Shamsuzzoha Bayzid. SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm |
| 0 | -- | 0 | Jian Zhang 0020, Sina Ghadermarzi, Akila Katuwawala, Lukasz A. Kurgan. DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences |
| 0 | -- | 0 | Xiao Cao, WenJia He, Zitan Chen, Yifan Li, Kexin Wang, Hongbo Zhang, Lesong Wei, LiZhen Cui, Ran Su, Leyi Wei. PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture |
| 0 | -- | 0 | Shuquan Rao, Ancha Baranova, Hongbao Cao, Jiu Chen, Xiangrong Zhang, Fuquan Zhang. Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption |
| 0 | -- | 0 | Yosef Masoudi-Sobhanzadeh, Aysan Salemi, Mohammad M. Pourseif, Behzad Jafari, Yadollah Omidi, Ali Masoudi-Nejad. Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries |
| 0 | -- | 0 | Ting Yu, Renmin Han, Zhaoyuan Fang, Zengchao Mu, Hongyu Zheng, Juntao Liu. TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs |
| 0 | -- | 0 | Patrick Brendan Timmons, Chandralal M. Hewage. APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures |
| 0 | -- | 0 | Junjie Wee, Kelin Xia. Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction |
| 0 | -- | 0 | Md. Rezanur Rahman, Tania Islam, Md Shahjaman, Md Rafiqul Islam, Salvo Danilo Lombardo, Placido Bramanti, Rosella Ciurleo, Alessia Bramanti, Andrey Tchorbanov, Francesco Fisicaro, Paolo Fagone, Ferdinando Nicoletti, Manuela Pennisi. Discovering common pathogenetic processes between COVID-19 and diabetes mellitus by differential gene expression pattern analysis |
| 0 | -- | 0 | Christoph A. Krettler, Gerhard G. Thallinger. A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics |
| 0 | -- | 0 | Florian Borchert, Andreas Mock, Aurelie Tomczak, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P. Schapranow. Knowledge bases and software support for variant interpretation in precision oncology |
| 0 | -- | 0 | Yoshihiro Noguchi, Tomoya Tachi, Hitomi Teramachi. Detection algorithms and attentive points of safety signal using spontaneous reporting systems as a clinical data source |
| 0 | -- | 0 | Yan Huang, Pingping Wang, Wenyang Zhou, Meng Luo, Zhaochun Xu, Rui Cheng, Chang Xu, Xiyun Jin, Yiqun Li, Qinghua Jiang. Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles |
| 0 | -- | 0 | Lu Wang, Boran Gao, Yue Fan, Fuzhong Xue, Xiang Zhou. Mendelian randomization under the omnigenic architecture |
| 0 | -- | 0 | Guangyuan Li, Balaji Iyer, V. B. Surya Prasath, Yizhao Ni, Nathan Salomonis. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity |