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BMC Bioinformatics

Published By BMC

  • BMC Bioinformatics: 2023, vol: 24, issue: 1
  • 1)- Elena Pianfetti, Marta Lovino, Elisa Ficarra, Loredana Martignetti. MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge. BMC bioinformatics. 2023, 24 (1): 443
    Cited : 1
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  • 2)- Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie, Ren Kong, Shan Chang. CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction. BMC bioinformatics. 2023, 24 (1): 444
    Cited : 2
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  • 3)- Valentina Nale, Alice Chiodi, Noemi Di Nanni, Ingrid Cifola, Marco Moscatelli, Cinzia Cocola, Matteo Gnocchi, Eleonora Piscitelli, Ada Sula, Ileana Zucchi, Rolland Reinbold, Luciano Milanesi, Alessandra Mezzelani, Paride Pelucchi, Ettore Mosca. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC bioinformatics. 2023, 24 (1): 445
    Cited : 0
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  • 4)- Anup Kumar, Björn Grüning, Rolf Backofen. Transformer-based tool recommendation system in Galaxy. BMC bioinformatics. 2023, 24 (1): 446
    Cited : 0
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  • 5)- Incheol Shin, Keumseok Kang, Juseong Kim, Sanghun Sel, Jeonghoon Choi, Jae-Wook Lee, Ho Young Kang, Giltae Song. AptaTrans: a deep neural network for predicting aptamer-protein interaction using pretrained encoders. BMC bioinformatics. 2023, 24 (1): 447
    Cited : 0
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  • 6)- Danyi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu, Qin Liu. Predicting anticancer synergistic drug combinations based on multi-task learning. BMC bioinformatics. 2023, 24 (1): 448
    Cited : 1
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  • 7)- Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari, Abdollah Allahvardi. Machine learning-based approaches for ubiquitination site prediction in human proteins. BMC bioinformatics. 2023, 24 (1): 449
    Cited : 2
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  • 8)- Nan Shao, Chenshuo Ren, Tianyuan Hu, Dianbing Wang, Xiaofan Zhu, Min Li, Tao Cheng, Yingchi Zhang, Xian-En Zhang. Detection of continuous hierarchical heterogeneity by single-cell surface antigen analysis in the prognosis evaluation of acute myeloid leukaemia. BMC bioinformatics. 2023, 24 (1): 450
    Cited : 0
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  • 9)- Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu, Lun Hu. Biocaiv: an integrative webserver for motif-based clustering analysis and interactive visualization of biological networks. BMC bioinformatics. 2023, 24 (1): 451
    Cited : 1
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  • 10)- He Zhao, Guixia Liu, Xintian Cao. A seed expansion-based method to identify essential proteins by integrating protein-protein interaction sub-networks and multiple biological characteristics. BMC bioinformatics. 2023, 24 (1): 452
    Cited : 1
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  • 11)- Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau, Ahmed Ashour Ahmed. Completing a genomic characterisation of microscopic tumour samples with copy number. BMC bioinformatics. 2023, 24 (1): 453
    Cited : 2
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  • 12)- Hui Sun, Yingfeng Zheng, Haonan Xie, Huidong Ma, Xiaoguang Liu, Gang Wang. PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering. BMC bioinformatics. 2023, 24 (1): 454
    Cited : 1
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  • 13)- Zhaoyan Ming, Xiangjun Chen, Shunlong Wang, Hong Liu, Zhiming Yuan, Minghui Wu, Han Xia. HostNet: improved sequence representation in deep neural networks for virus-host prediction. BMC bioinformatics. 2023, 24 (1): 455
    Cited : 0
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  • 14)- Hanhan Cong, Hong Liu, Yi Cao, Cheng Liang, Yuehui Chen. Protein-protein interaction site prediction by model ensembling with hybrid feature and self-attention. BMC bioinformatics. 2023, 24 (1): 456
    Cited : 2
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  • 15)- Eduardo N Castanho, João P Lobo, Rui Henriques, Sara C Madeira. G-bic: generating synthetic benchmarks for biclustering. BMC bioinformatics. 2023, 24 (1): 457
    Cited : 2
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  • 16)- P Kavitha, G Ayyappan, Prabhu Jayagopal, Sandeep Kumar Mathivanan, Saurav Mallik, Amal Al-Rasheed, Mohammed S Alqahtani, Ben Othman Soufiene. Detection for melanoma skin cancer through ACCF, BPPF, and CLF techniques with machine learning approach. BMC bioinformatics. 2023, 24 (1): 458
    Cited : 1
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  • 17)- Abdelkader Behdenna, Maximilien Colange, Julien Haziza, Aryo Gema, Guillaume Appé, Chloé-Agathe Azencott, Akpéli Nordor. pyComBat, a Python tool for batch effects correction in high-throughput molecular data using empirical Bayes methods. BMC bioinformatics. 2023, 24 (1): 459
    Cited : 10
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  • 18)- Xuechun Xu, Nayanika Bhalla, Patrik Ståhl, Joakim Jaldén. Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network. BMC bioinformatics. 2023, 24 (1): 461
    Cited : 2
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  • 19)- Yiyun Rao, Nabeel Ahmed, Justin Pritchard, Edward P O'Brien. Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. BMC bioinformatics. 2023, 24 (1): 462
    Cited : 0
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  • 20)- Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang, Haoyang Cai. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. BMC bioinformatics. 2023, 24 (1): 463
    Cited : 0
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  • 21)- Ying Li, Xiao-Ou Zhang, Yan Liu, Aiping Lu. Allele-specific binding (ASB) analyzer for annotation of allele-specific binding SNPs. BMC bioinformatics. 2023, 24 (1): 464
    Cited : 1
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  • 22)- Youpeng Yang, Qiuhong Zeng, Gaotong Liu, Shiyao Zheng, Tianyang Luo, Yibin Guo, Jia Tang, Yi Huang. Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer. BMC bioinformatics. 2023, 24 (1): 465
    Cited : 0
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  • 23)- Joseph Hellerstein. An oscillating reaction network with an exact closed form solution in the time domain. BMC bioinformatics. 2023, 24 (1): 466
    Cited : 0
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  • 24)- Min Zhang, Chengkui Zhao, Qi Cheng, Jiayu Xu, Nan Xu, Lei Yu, Weixing Feng. A score-based method of immune status evaluation for healthy individuals with complete blood cell counts. BMC bioinformatics. 2023, 24 (1): 467
    Cited : 2
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  • 25)- Jason D Limberis, John Z Metcalfe. primerJinn: a tool for rationally designing multiplex PCR primer sets for amplicon sequencing and performing in silico PCR. BMC bioinformatics. 2023, 24 (1): 468
    Cited : 1
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  • 26)- Konstantin Weissenow, Burkhard Rost. Rendering protein mutation movies with MutAmore. BMC bioinformatics. 2023, 24 (1): 469
    Cited : 0
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  • 27)- Xiaojun Hu, Oscar P Hurtado-Gonzales, Bishwo N Adhikari, Ronald D French-Monar, Martha Malapi, Joseph A Foster, Clint D McFarland. PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data. BMC bioinformatics. 2023, 24 (1): 470
    Cited : 1
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  • 28)- Mary O Richardson, Sean R Eddy. ORFeus: a computational method to detect programmed ribosomal frameshifts and other non-canonical translation events. BMC bioinformatics. 2023, 24 (1): 471
    Cited : 0
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  • 29)- Omar Abdelwahab, François Belzile, Davoud Torkamaneh. Performance analysis of conventional and AI-based variant callers using short and long reads. BMC bioinformatics. 2023, 24 (1): 472
    Cited : 4
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  • 30)- Jiahui Wu, Bo Liu, Jidong Zhang, Zhihan Wang, Jianqiang Li. DL-PPI: a method on prediction of sequenced protein-protein interaction based on deep learning. BMC bioinformatics. 2023, 24 (1): 473
    Cited : 5
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  • 31)- Amrita Chattopadhyay, Chien-Yueh Lee, Ya-Chin Lee, Chiang-Lin Liu, Hsin-Kuang Chen, Yung-Hua Li, Liang-Chuan Lai, Mong-Hsun Tsai, Yen-Hsuan Ni, Han-Mo Chiu, Tzu-Pin Lu, Eric Y Chuang. Twnbiome: a public database of the healthy Taiwanese gut microbiome. BMC bioinformatics. 2023, 24 (1): 474
    Cited : 1
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  • 32)- Min Hyung Cho, Kwang-Hwi Cho, Kyoung Tai No. PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing. BMC bioinformatics. 2023, 24 (1): 475
    Cited : 0
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  • 33)- Shanghui Lu, Yong Liang, Le Li, Rui Miao, Shuilin Liao, Yongfu Zou, Chengjun Yang, Dong Ouyang. Predicting potential microbe-disease associations based on auto-encoder and graph convolution network. BMC bioinformatics. 2023, 24 (1): 476
    Cited : 1
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  • 34)- Diana Zarei, Amene Saghazadeh, Nima Rezaei. Subtyping irritable bowel syndrome using cluster analysis: a systematic review. BMC bioinformatics. 2023, 24 (1): 478
    Cited : 0
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  • 35)- Rajul Mahto, Saboor Uddin Ahmed, Rizwan Ur Rahman, Rabia Musheer Aziz, Priyanka Roy, Saurav Mallik, Aimin Li, Mohd Asif Shah. A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection. BMC bioinformatics. 2023, 24 (1): 479
    Cited : 12
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  • 36)- Yining Liu, Yinuo Jin, Elham Azizi, Andrew J Blumberg. Cellstitch: 3D cellular anisotropic image segmentation via optimal transport. BMC bioinformatics. 2023, 24 (1): 480
    Cited : 1
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  • 37)- Zhen-Hao Guo, Yan Wu, Siguo Wang, Qinhu Zhang, Jin-Ming Shi, Yan-Bin Wang, Zhan-Heng Chen. scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data. BMC bioinformatics. 2023, 24 (1): 481
    Cited : 0
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  • 38)- Michael J Kane, Casey King, Denise Esserman, Nancy K Latham, Erich J Greene, David A Ganz. A compressed large language model embedding dataset of ICD 10 CM descriptions. BMC bioinformatics. 2023, 24 (1): 482
    Cited : 1
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  • 39)- Chenqi Liao, Xiong Wang. TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data. BMC bioinformatics. 2023, 24 (1): 483
    Cited : 11
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  • 40)- Yingke Yang, Peiluan Li. GPDRP: a multimodal framework for drug response prediction with graph transformer. BMC bioinformatics. 2023, 24 (1): 484
    Cited : 3
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  • 41)- Daniel Marrama, William D Chronister, Luise Westernberg, Randi Vita, Zeynep Koşaloğlu-Yalçın, Alessandro Sette, Morten Nielsen, Jason A Greenbaum, Bjoern Peters. PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. BMC bioinformatics. 2023, 24 (1): 485
    Cited : 3
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  • 42)- Xiangwen Zheng, Xuanze Wang, Xiaowei Luo, Fan Tong, Dongsheng Zhao. BioEGRE: a linguistic topology enhanced method for biomedical relation extraction based on BioELECTRA and graph pointer neural network. BMC bioinformatics. 2023, 24 (1): 486
    Cited : 0
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  • 43)- Kateřina Faltejsková, Jiří Vondrášek. PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. BMC bioinformatics. 2023, 24 (1): 487
    Cited : 0
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  • 44)- Warith Eddine Djeddi, Khalil Hermi, Sadok Ben Yahia, Gayo Diallo. Advancing drug-target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining. BMC bioinformatics. 2023, 24 (1): 488
    Cited : 8
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  • 45)- Miaoshan Lu, Hengxuan Jiang, Ruimin Wang, Shaowei An, Jiawei Wang, Changbin Yu. Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation. BMC bioinformatics. 2023, 24 (1): 489
    Cited : 0
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  • 46)- Xiaomeng Zhang, Hongtao Zhang, Zhihao Wang, Xiaofei Ma, Jiancheng Luo, Yingying Zhu. PWSC: a novel clustering method based on polynomial weight-adjusted sparse clustering for sparse biomedical data and its application in cancer subtyping. BMC bioinformatics. 2023, 24 (1): 490
    Cited : 0
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  • 47)- Daniel Dorey-Robinson, Giuseppe Maccari, John A Hammond. IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics. BMC bioinformatics. 2023, 24 (1): 491
    Cited : 0
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  • 48)- Thummarat Paklao, Apichat Suratanee, Kitiporn Plaimas. ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology. BMC bioinformatics. 2023, 24 (1): 492
    Cited : 1
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