Journal: Briefings in Bioinformatics

Volume 22, Issue 3

0 -- 0Zicheng Zhang, Siqi Bao, Congcong Yan, Ping Hou, Meng Zhou 0003, Jie Sun 0021. Computational principles and practice for decoding immune contexture in the tumor microenvironment
0 -- 0Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu. Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes
0 -- 0Yuchen Yang, Gang Li, Huijun Qian, Kirk C. Wilhelmsen, Yin Shen, Yun Li. SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection
0 -- 0Hengqiang Zhao, Shanshan Gu, Siqi Bao, Congcong Yan, Zicheng Zhang, Ping Hou, Meng Zhou 0003, Jie Sun 0021. Mechanistically derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer
0 -- 0Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li. DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites
0 -- 0Hung Nguyen, Duc Tran, Bang Tran, Bahadir Pehlivan, Tin Nguyen 0001. A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data
0 -- 0Ruiling Fang, Haitao Yang, Yuzhao Gao, Hongyan Cao, Ellen L. Goode, Yuehua Cui. Gene-based mediation analysis in epigenetic studies
0 -- 0Zhongqi Wen, Cheng Yan, Guihua Duan, Suning Li, Fang-Xiang Wu, Jianxin Wang 0001. A survey on predicting microbe-disease associations: biological data and computational methods
0 -- 0Xin Wu, Hao Zheng, Zuochao Dou, Feng Chen 0016, Jieren Deng, Xiang Chen, Shengqian Xu, Guanmin Gao, Mengmeng Li, Zhen Wang, Yuhui Xiao, Kang Xie, Shuang Wang 0002, Huji Xu. A novel privacy-preserving federated genome-wide association study framework and its application in identifying potential risk variants in ankylosing spondylitis
0 -- 0Minzhe Zhang, Thomas Sheffield, Xiaowei Zhan, Qiwei Li, Donghan M. Yang, Yunguan Wang, Shidan Wang, Yang Xie, Tao Wang, Guanghua Xiao. Spatial molecular profiling: platforms, applications and analysis tools
0 -- 0Hua Tan, Pora Kim, Peiqing Sun, Xiaobo Zhou 0001. miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer
0 -- 0Jing Chen, Lindsey J. Leach, Zewei Luo. Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species
0 -- 0Wei Wang, Qiuying Dai, Fang Li, Yi Xiong, Dong-Qing Wei. MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs
0 -- 0Xiaohui Niu, Kaixuan Deng, Lifen Liu, Kun Yang, Xuehai Hu. A statistical framework for predicting critical regions of p53-dependent enhancers
0 -- 0Arjun Bhattacharya, Alina M. Hamilton, Helena Furberg, Eugene Pietzak, Mark P. Purdue, Melissa A. Troester, Katherine A. Hoadley, Michael I. Love. An approach for normalization and quality control for NanoString RNA expression data
0 -- 0Hang Wei, Yong Xu 0001, Bin Liu 0014. iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning
0 -- 0Huaming Chen, Fuyi Li, Lei Wang 0001, Yaochu Jin, Chi-Hung Chi, Lukasz A. Kurgan, Jiangning Song, Jun Shen 0001. Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions
0 -- 0Kangning Dong, Shihua Zhang. Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data
0 -- 0Joanna Miskiewicz, Joanna Sarzynska, Marta Szachniuk. How bioinformatics resources work with G4 RNAs
0 -- 0Pan Wang, Qi Li, Nan Sun, Yibo Gao, Jun S. Liu, Ke Deng, Jie He. MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model
0 -- 0Mattia Forcato, Oriana Romano, Silvio Bicciato. Computational methods for the integrative analysis of single-cell data
0 -- 0Luciano A. Abriata, Matteo Dal Peraro. State-of-the-art web services for de novo protein structure prediction
0 -- 0Murilo Horacio Pereira da Cruz, Douglas Silva Domingues, Priscila Tiemi Maeda Saito, Alexandre Rossi Paschoal, Pedro Henrique Bugatti. TERL: classification of transposable elements by convolutional neural networks
0 -- 0Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma 0003, Bingqiang Liu. The functional determinants in the organization of bacterial genomes
0 -- 0Stephan Struckmann, Mathias Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Möller. Scoring functions for drug-effect similarity
0 -- 0Veronica Porubsky, Lucian P. Smith, Herbert M. Sauro. Publishing reproducible dynamic kinetic models
0 -- 0Ruidong Li, Shibo Wang, Yanru Cui, Han Qu, John M. Chater, Le Zhang, Julong Wei, Meiyue Wang, Yang Xu, Lei Yu, Jianming Lu, Yuanfa Feng, Rui Zhou, Yuhan Huang, Renyuan Ma, Jianguo Zhu 0003, Wei-De Zhong, Zhenyu Jia. Extended application of genomic selection to screen multiomics data for prognostic signatures of prostate cancer
0 -- 0Jialin Zhang, Da Xu, Kaijing Hao, Yusen Zhang, Wei Chen, Jiaguo Liu, Rui Gao, Chuanyan Wu, Yang De Marinis. FS-GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT
0 -- 0Lei Xu, Shanshan Jiang, Jin Wu, Quan Zou 0001. An in silico approach to identification, categorization and prediction of nucleic acid binding proteins
0 -- 0Hartmut Foerster, James N. D. Battey, Nicolas Sierro, Nikolai V. Ivanov, Lukas A. Mueller. Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook
0 -- 0Anjali Garg, Neelja Singhal, Manish Kumar 0005. Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach
0 -- 0Xing-Xing Shi, Feng-Xu Wu, Long-Can Mei, Yu-Liang Wang, Ge-Fei Hao, Guangfu Yang. Bioinformatics toolbox for exploring protein phosphorylation network
0 -- 0Tingting Gong, Vanessa M. Hayes, Eva K. F. Chan. Detection of somatic structural variants from short-read next-generation sequencing data
0 -- 0Cécile Hilpert, Geneviève Bricheux, Didier Debroas. Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow?
0 -- 0Wenwen Mei, Zhiwen Jiang, Yang Chen, Li Chen, Aziz Sancar, Yuchao Jiang. Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines
0 -- 0Xing Chen 0001, Tian-Hao Li, Yan Zhao, Chun-Chun Wang, Chi-Chi Zhu. Deep-belief network for predicting potential miRNA-disease associations
0 -- 0Piyush Agrawal, Dhruv Bhagat, Manish Mahalwal, Neelam Sharma, Gajendra P. S. Raghava. AntiCP 2.0: an updated model for predicting anticancer peptides
0 -- 0Jie Huang, Jiazhou Chen, Bin Zhang, Lei Zhu, Hongmin Cai. Evaluation of gene-drug common module identification methods using pharmacogenomics data
0 -- 0Yi-Heng Zhu, Jun Hu 0010, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-jun Yu. Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features
0 -- 0Eva S. Deutekom, Berend Snel, Teunis J. P. van Dam. Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes
0 -- 0MengYun Wu, Huangdi Yi, Shuangge Ma. Vertical integration methods for gene expression data analysis
0 -- 0Chunlong Zhang, Ning Zhao, Xue Zhang, Jun Xiao, Junyi Li, Dezhong Lv, Weiwei Zhou, Yongsheng Li, Juan Xu, Xia Li. SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis
0 -- 0Min Yuan, Xu Steven Xu, Yaning Yang, Yinsheng Zhou, Yi Li, Jinfeng Xu, Jose Pinheiro. SCEBE: an efficient and scalable algorithm for genome-wide association studies on longitudinal outcomes with mixed-effects modeling
0 -- 0Mingyi Liu, Ashok Dongre. Proper imputation of missing values in proteomics datasets for differential expression analysis
0 -- 0Jieming Chen, Shravan Madireddi, Deepti Nagarkar, Maciej Migdal, Jason A. Vander Heiden, Diana Chang, Kiran Mukhyala, Suresh Selvaraj, Edward E. Kadel, Matthew J. Brauer, Sanjeev Mariathasan, Julie Hunkapiller, Suchit Jhunjhunwala, Matthew L. Albert, Christian Hammer. In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales
0 -- 0Arif Canakoglu, Pietro Pinoli, Andrea Gulino, Luca Nanni, Marco Masseroli, Stefano Ceri. Federated sharing and processing of genomic datasets for tertiary data analysis
0 -- 0Jen-Hao Chen, Yufeng Jane Tseng. Different molecular enumeration influences in deep learning: an example using aqueous solubility
0 -- 0Denis Awany, Emile R. Chimusa. Heritability jointly explained by host genotype and microbiome: will improve traits prediction?
0 -- 0Fei-Fei Hu, Chun-Jie Liu, Lan-Lan Liu, Qiong Zhang, An-Yuan Guo. Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response
0 -- 0Shihua Zhang, Xiaolong He, Rui Zhang, Wensheng Deng. LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events
0 -- 0Zi-Yi Yang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao. Scopy: an integrated negative design python library for desirable HTS/VS database design
0 -- 0Cindy Perscheid. Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches
0 -- 0Soyeon Kim, Yulong Bai, Zhenjiang Fan, Brenda Diergaarde, George C. Tseng, Hyun Jung Park. The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer
0 -- 0Cátia Vaz, Marta Nascimento, João A. Carriço, Tatiana Rocher, Alexandre P. Francisco. Distance-based phylogenetic inference from typing data: a unifying view
0 -- 0Rodrigo Madurga, Noemí García-Romero, Beatriz Jiménez, Ana Collazo, Francisco Pérez-Rodríguez, Aurelio Hernández-Laín, Carlos Fernández-Carballal, Ricardo Prat-Acín, Massimiliano Zanin, Ernestina Menasalvas, Ángel Ayuso-Sacido. Normal tissue content impact on the GBM molecular classification
0 -- 0Kun Sun 0003, Huating Wang, Hao Sun 0001. NAMS webserver: coding potential assessment and functional annotation of plant transcripts
0 -- 0A. K. M. Azad, Mojdeh Dinarvand, Alireza Nematollahi, Joshua Swift, Louise Lutze-Mann, Fatemeh Vafaee. A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond
0 -- 0DoHoon Lee, Youngjune Park, Sun Kim. Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches
0 -- 0Guo-Li Xiong, Wen-Ling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao. Improving structure-based virtual screening performance via learning from scoring function components
0 -- 0Peng Zhang, Mingyue Liu, Ya Cui, Pan Zheng, Yang Liu. Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers
0 -- 0Zerong Wang, Dongyang Liu, Baofang Xu, Ruixia Tian, Yongchun Zuo. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins
0 -- 0Haitao Yang, Zhaohong Deng, Xiaoyong Pan, Hong-bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang 0001, Jing Wu. RNA-binding protein recognition based on multi-view deep feature and multi-label learning
0 -- 0Rong Li, Xue Huang, Xiao Liang, Min Su, Keng Po Lai, Jian Chen. Integrated omics analysis reveals the alteration of gut microbe-metabolites in obese adults
0 -- 0Sendong Zhao, Chang Su, Zhiyong Lu, Fei Wang 0001. Recent advances in biomedical literature mining
0 -- 0Junyi Chen, Ka Chun Wong. RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets
0 -- 0Louison Fresnais, Pedro J. Ballester. The impact of compound library size on the performance of scoring functions for structure-based virtual screening
0 -- 0Jan Zaucha, Michael Heinzinger, A. Kulandaisamy, Evans Kataka, Óscar Llorian Salvádor, Petr Popov, Burkhard Rost, M. Michael Gromiha, Boris S. Zhorov, Dmitrij Frishman. Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins
0 -- 0Chun-Chun Wang, Yan Zhao, Xing Chen 0001. Drug-pathway association prediction: from experimental results to computational models
0 -- 0Cristian D. Loaiza, Naveen Duhan, Matthew Lister, Rakesh Kaundal. In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets
0 -- 0Zhe Wang, Lei Meng, Hong Liu, Liang Shen, Hong-Fang Ji. AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer's disease
0 -- 0Wenbo Guo, Dongfang Wang, Shicheng Wang, Yiran Shan, Changyi Liu, Jin Gu. scCancer: a package for automated processing of single-cell RNA-seq data in cancer
0 -- 0Surui Pei, Tao Liu, Xue Ren, Weizhong Li, Chongjian Chen, Zhi Xie. Benchmarking variant callers in next-generation and third-generation sequencing analysis
0 -- 0Hao Fei 0001, Yafeng Ren, Yue Zhang 0004, Donghong Ji, Xiaohui Liang. Enriching contextualized language model from knowledge graph for biomedical information extraction
0 -- 0Dingfeng Wu, Wenxing Gao, Xiaoyi Li, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu, Guoqing Zhang, Ruixin Zhu. Dr AFC: drug repositioning through anti-fibrosis characteristic
0 -- 0Shibo Wang, Yang Xu, Han Qu, Yanru Cui, Ruidong Li, John M. Chater, Lei Yu, Rui Zhou, Renyuan Ma, Yuhan Huang, Yiru Qiao, Xuehai Hu, Weibo Xie, Zhenyu Jia. Boosting predictabilities of agronomic traits in rice using bivariate genomic selection
0 -- 0Jinzhuang Dou, Degang Wu, Lin Ding, Kai Wang, Minghui Jiang 0005, Xiaoran Chai, Dermot F. Reilly, E. Shyong Tai, Jianjun Liu, Xueling Sim, Shanshan Cheng, Chaolong Wang. Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction
0 -- 0Jian Yi, Longyun Chen, Yajie Xiao, Zhikun Zhao, Xiaofan Su. Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools
0 -- 0Zhenyu Yue, Xinlu Chu, Junfeng Xia. PredCID: prediction of driver frameshift indels in human cancer
0 -- 0Duyen Thi Do, Trang Thanh Quynh Le, Nguyen-Quoc-Khanh Le. Using deep neural networks and biological subwords to detect protein S-sulfenylation sites
0 -- 0Hua-Ping Liu, Hung-Ming Lai, Zheng Guo 0002. Prostate cancer early diagnosis: circulating microRNA pairs potentially beyond single microRNAs upon 1231 serum samples
0 -- 0Aleksandra E. Badaczewska-Dawid, Sebastian Kmiecik, Michal Kolinski. Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement
0 -- 0Vincenzo Bonnici, Emiliano Maresi, Rosalba Giugno. Challenges in gene-oriented approaches for pangenome content discovery
0 -- 0Yulan Deng, Hao Luo, Zhenyu Yang, Lunxu Liu. LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers
0 -- 0Rong Li, Chao Guo, Yu Li, Zuqian Qin, Wenjun Huang. Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study
0 -- 0Xuanyi Wang, Zixuan Chai, Guizhi Pan, Youjin Hao, Bo Li, Ting Ye, Yinghong Li 0002, Fei Long, Lixin Xia, Mingwei Liu. ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer
0 -- 0Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu. Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature
0 -- 0Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu 0035, Dong-Sheng Cao, Tingjun Hou. Beware of the generic machine learning-based scoring functions in structure-based virtual screening
0 -- 0Dan Wang, Fei-Liao Lai, Feng Gao 0001. Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae
0 -- 0Xiaopeng Jin, Qing Liao 0001, Bin Liu 0014. PL-search: a profile-link-based search method for protein remote homology detection
0 -- 0Nan Sheng, Hui Cui, Tiangang Zhang, Ping Xuan. Attentional multi-level representation encoding based on convolutional and variance autoencoders for lncRNA-disease association prediction
0 -- 0Cong Feng, Min Dai, Yongjing Liu, Ming Chen 0005. Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage
0 -- 0Ye Wang, Tathagata Bhattacharya, Yuchao Jiang, Xiao Qin 0001, Yue Wang, Yunlong Liu, Andrew J. Saykin, Li Chen. A novel deep learning method for predictive modeling of microbiome data
0 -- 0Zheyang Zhang, Sainan Zhang, Xin Li, Zhangxiang Zhao, Changjing Chen, Juxuan Zhang, Mengyue Li, Zixin Wei, Wenbin Jiang, Bo Pan, Ying Li, Yixin Liu, Yingyue Cao, Wenyuan Zhao, Yunyan Gu, Yan Yu, Qingwei Meng, Lishuang Qi. Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma
0 -- 0Jike Wang, Dong-Sheng Cao, Cunchen Tang, Lei Xu 0035, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun, Tingjun Hou. DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges
0 -- 0Hao-Dong Xu, Peilin Jia, Zhongming Zhao. Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning
0 -- 0Shuang Deng, Hongwan Zhang, Kaiyu Zhu, Xingyang Li, Ying Ye, Rui Li, Xuefei Liu, Dongxin Lin, Zhixiang Zuo, Jian Zheng. M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers
0 -- 0Yan Zhao, Chun-Chun Wang, Xing Chen 0001. Microbes and complex diseases: from experimental results to computational models
0 -- 0Jianan Wang, Su Chen, Lili Dong, Guohua Wang. CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table
0 -- 0Harold Duruflé, Merwann Selmani, Philippe Ranocha, Elisabeth Jamet, Christophe Dunand, Sébastien Déjean. A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis
0 -- 0Yahui Long, Jiawei Luo, Yu Zhang, Yan Xia. Predicting human microbe-disease associations via graph attention networks with inductive matrix completion
0 -- 0Lei Zheng, Dongyang Liu, Wuritu Yang, Lei Yang, Yongchun Zuo. RaacLogo: a new sequence logo generator by using reduced amino acid clusters
0 -- 0Xiangyu Luo, Joel Schwartz, Andrea A. Baccarelli, Zhonghua Liu. Testing cell-type-specific mediation effects in genome-wide epigenetic studies
0 -- 0Mingxuan Gao, Mingyi Ling, Xinwei Tang, Shun Wang, Xu Xiao, Ying Qiao, Wenxian Yang, Rongshan Yu. Comparison of high-throughput single-cell RNA sequencing data processing pipelines
0 -- 0Jiangyi Shao, Ke Yan 0003, Bin Liu. FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network
0 -- 0Haopeng Yu, Yi Zhang, Qing Sun, Huijie Gao, Shiheng Tao. RSVdb: a comprehensive database of transcriptome RNA structure
0 -- 0Chunyu Yu, Boyan Shen, Kaiqiang You, Qi Huang, Minglei Shi, Congying Wu, Yang Chen, Chaolin Zhang, Tingting Li. Proteome-scale analysis of phase-separated proteins in immunofluorescence images
0 -- 0Hsin-Yao Wang, Chia-Ru Chung, Zhuo Wang, Shangfu Li, Bo-Yu Chu, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee. A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra
0 -- 0Yi Hsiao, Bo-Han Su, Yufeng J. Tseng. Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development
0 -- 0Qiong Zhang, Mei Luo, Chun-Jie Liu, An-Yuan Guo. CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles
0 -- 0Leandro A Bugnon, Cristian A. Yones, Diego H. Milone, Georgina Stegmayer. Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning
0 -- 0Gunnar Völkel, Simon Laban, Axel Fürstberger, Silke D. Kühlwein, Nensi Ikonomi, Thomas K. Hoffman, Cornelia Brunner, Donna S. Neuberg, Verena Gaidzik, Hartmut Döhner, Johann M. Kraus, Hans A. Kestler. Analysis, identification and visualization of subgroups in genomics
0 -- 0Ran Wei, Pengcheng Li, Funan He, Gang Wei, Zhan Zhou, Zhixi Su, Ting Ni. Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers
0 -- 0Xiaoqing Peng, Hong-Dong Li, Fang-Xiang Wu, Jianxin Wang 0001. Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics
0 -- 0Pedro G. Nachtigall, André Y. Kashiwabara, Alan M. Durham. CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts
0 -- 0Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang 0003, Qiankun Wang, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei. DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method
0 -- 0Zhixu Qiu, Siyuan Chen, Yuhong Qi, Chunni Liu, Jingjing Zhai, Shang Xie, Chuang Ma. Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS
0 -- 0John Torcivia-Rodriguez, Raja Mazumder. Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples
0 -- 0Pawel Dabrowski-Tumanski, Pawel Rubach, Wanda Niemyska, Bartosz Ambrozy Gren, Joanna I. Sulkowska. Topoly: Python package to analyze topology of polymers
0 -- 0Yu-An Huang, Keith C. C. Chan, Zhu-Hong You, Pengwei Hu, Lei Wang 0121, Zhi-an Huang. Predicting microRNA-disease associations from lncRNA-microRNA interactions via Multiview Multitask Learning
0 -- 0Chen Yang, Xiaowen Huang, Yan Li, Junfei Chen, Yuanyuan Lv, Shixue Dai. Prognosis and personalized treatment prediction in TP53-mutant hepatocellular carcinoma: an in silico strategy towards precision oncology
0 -- 0Meng Zhou 0003, Zicheng Zhang, Siqi Bao, Ping Hou, Congcong Yan, Jianzhong Su, Jie Sun 0021. Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer
0 -- 0Jiawei Li, Yuqian Pu, Jijun Tang, Quan Zou 0001, Fei Guo. DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences
0 -- 0Qifeng Bai, Shuoyan Tan, Tingyang Xu, Huanxiang Liu, JunZhou Huang, Xiaojun Yao. MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm
0 -- 0Amlan Talukder, Clayton Barham, Xiaoman Li, Haiyan Hu. Interpretation of deep learning in genomics and epigenomics
0 -- 0Moritz Herrmann, Philipp Probst, Roman Hornung, Vindi Jurinovic, Anne-Laure Boulesteix. Large-scale benchmark study of survival prediction methods using multi-omics data
0 -- 0Aman Chandra Kaushik, Yan-Jing Wang, Xiangeng Wang, Dong-Qing Wei. Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations
0 -- 0Vivek Dhar Dwivedi, Aditya Arya, Pardeep Yadav, Rajesh Kumar, Vinod Kumar, Gajendra P. S. Raghava. DenvInD: dengue virus inhibitors database for clinical and molecular research
0 -- 0Dionysios Fanidis, Panagiotis Moulos. Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis
0 -- 0Anna Marabotti, Bernardina Scafuri, Angelo M. Facchiano. Predicting the stability of mutant proteins by computational approaches: an overview
0 -- 0Hukam C. Rawal, Ulavappa B. Angadi, Tapan Kumar Mondal. TEnGExA: an R package based tool for tissue enrichment and gene expression analysis
0 -- 0Jing Tang, Minjie Mou, Yunxia Wang, Yongchao Luo, Feng Zhu 0004. MetaFS: Performance assessment of biomarker discovery in metaproteomics
0 -- 0Vu Viet Hoang Pham, Xiaomei Li, Buu Minh Thanh Truong, Thin Nguyen, Lin Liu 0003, Jiuyong Li, Thuc Duy Le. The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge
0 -- 0Zhuohui Wei, Yue Zhang, Wanlin Weng, Jiazhou Chen, Hongmin Cai. Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets
0 -- 0Yanhong Huang, Xiao Chang, Yu Zhang, Luonan Chen, Xiaoping Liu 0002. Disease characterization using a partial correlation-based sample-specific network
0 -- 0Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao. Landscape of drug-resistance mutations in kinase regulatory hotspots
0 -- 0Shuai Jiang, Hao Li 0035, Hao Hong, Guifang Du, Xin Huang, Yu Sun, Junting Wang, Huan Tao, Kang Xu, Cheng Li, Yang Chen, Hebing Chen, Xiaochen Bo. Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains
0 -- 0Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang. DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy
0 -- 0Zhi-Luo Deng, Akshay Dhingra, Adrian Fritz, Jasper Götting, Philipp C. Münch, Lars Steinbrück, Thomas F. Schulz, Tina Ganzenmüller, Alice C. McHardy. Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses
0 -- 0Md. Mehedi Hasan 0002, Shaherin Basith, Mst. Shamima Khatun, Gwang Lee, Balachandran Manavalan, Hiroyuki Kurata. Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework
0 -- 0Qingfeng Zhang, Kai Yu, Shihua Li, Xiaolong Zhang, Qi Zhao, Xia Zhao, Zekun Liu, Han Cheng, Zexian Liu, Xiaoxing Li. gutMEGA: a database of the human gut MEtaGenome Atlas
0 -- 0Andrea Binatti, Silvia Bresolin, Stefania Bortoluzzi, Alessandro Coppe. iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data
0 -- 0Debby D. Wang, Mengxu Zhu, Hong Yan 0001. Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions
0 -- 0Mengying Zhang, Xiyun Jin, Junyi Li, Yi Tian, Qi Wang, Xinhui Li, Juan Xu, Yongsheng Li, Xia Li 0004. CeRNASeek: an R package for identification and analysis of ceRNA regulation
0 -- 0Jiangyi Shao, Bin Liu. ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm
0 -- 0Feng Huang, Xiang Yue, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang 0008. Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations
0 -- 0Hao-Dong Xu, Ru-Ping Liang, You-Gan Wang, Jian-Ding Qiu. mUSP: a high-accuracy map of the in situ crosstalk of ubiquitylation and SUMOylation proteome predicted via the feature enhancement approach
0 -- 0Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Jan Brezovsky. Recent advances in user-friendly computational tools to engineer protein function
0 -- 0Chuanjie Zhang, Tianhe Chen, Zongtai Li, Ao Liu, Yang Xu, Yi Gao, Danfeng Xu. Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts
0 -- 0Jianteng Zhou, Jianing Gao, Huan Zhang, Daren Zhao, Ao Li, Furhan Iqbal, Qinghua Shi, Yuanwei Zhang. PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data