BMC Bioinform.

Keyphrases

Publications

volume 24, number 1, 2023

Brian Kwan, Tobias Fuhrer, Daniel Montemayor, Jeffery C. Fink, Jiang He, Chi-yuan Hsu, Karen Messer, Robert G. Nelson, Minya Pu, Ana C. Ricardo, Hernan Rincon-Choles, Vallabh O. Shah, Hongping Ye, Jing Zhang, Kumar Sharma, Loki Natarajan
A generalized covariate-adjusted top-scoring pair algorithm with applications to diabetic kidney disease stage classification in the Chronic Renal Insufficiency Cohort (CRIC) Study. BMC Bioinform. 24 (1) (2023)
Luis F. Paulin, Muthuswamy Raveendran, R. Alan Harris, Jeffrey Rogers, Arndt von Haeseler, Fritz J. Sedlazeck
SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinform. 24 (1) (2023)
Wei Peng, Rong Wu, Wei Dai, Ning Yu
Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism. BMC Bioinform. 24 (1) (2023)
Jiaxing Chen, Yen Kaow Ng, Lu Lin, Xianglilan Zhang, Shuaicheng Li
On triangle inequalities of correlation-based distances for gene expression profiles. BMC Bioinform. 24 (1) (2023)
Emmanuel P. Mwanga, Doreen J. Siria, Joshua Mitton, Issa H. Mshani, Mario González-Jiménez, Prashanth Selvaraj, Klaas Wynne, Francesco Baldini, Fredros O. Okumu, Simon A. Babayan
Using transfer learning and dimensionality reduction techniques to improve generalisability of machine-learning predictions of mosquito ages from mid-infrared spectra. BMC Bioinform. 24 (1) (2023)
Shiva Afshar, Patricia R. Braun, Shizhong Han, Ying Lin
A multimodal deep learning model to infer cell-type-specific functional gene networks. BMC Bioinform. 24 (1) (2023)
Hoseung Song, Wodan Ling, Ni Zhao, Anna M. Plantinga, Courtney A. Broedlow, Nichole R. Klatt, Tiffany Hensley-McBain, Michael C. Wu
Accommodating multiple potential normalizations in microbiome associations studies. BMC Bioinform. 24 (1) (2023)
Ping Zhang, Weicheng Sun, Dengguo Wei, Guodong Li, Jinsheng Xu, Zhuhong You, Bowei Zhao, Li Li
PDA-PRGCN: identification of Piwi-interacting RNA-disease associations through subgraph projection and residual scaling-based feature augmentation. BMC Bioinform. 24 (1) (2023)
Jianjun Zhang, Xiaoyu Liang, Samantha Gonzales, Jianguo Liu, Xiaoyi Raymond Gao, Xuexia Wang
A gene based combination test using GWAS summary data. BMC Bioinform. 24 (1) (2023)
Yauheniya Zhdanovich, Jörg Ackermann, Peter J. Wild, Jens Köllermann, Katrin Bankov, Claudia Döring, Nadine Flinner, Henning Reis, Mike Wenzel, Benedikt Höh, Philipp Mandel, Thomas J. Vogl, Patrick Harter, Katharina Filipski, Ina Koch, Simon Bernatz
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology. BMC Bioinform. 24 (1) (2023)
Qing Ma, Yaqin Tan, Lei Wang
GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier. BMC Bioinform. 24 (1) (2023)
Xuehan Liu, Md Rakibul Hasan, Khandaker Asif Ahmed, Md. Zakir Hossain
Machine learning to analyse omic-data for COVID-19 diagnosis and prognosis. BMC Bioinform. 24 (1) (2023)
Jingwen Suo, Lize Gu, Xingyu Yan, Sijia Yang, Xiaoya Hu, Licheng Wang
PP-DDP: a privacy-preserving outsourcing framework for solving the double digest problem. BMC Bioinform. 24 (1) (2023)
Yang Yu, Yanyan Sun, Zhaoxian Li, Jiang Li, Dazhi Tian
Systematic analysis identifies XRCC4 as a potential immunological and prognostic biomarker associated with pan-cancer. BMC Bioinform. 24 (1) (2023)
Lingzhi Hu, Chengzhou Fu, Zhonglu Ren, Yongming Cai, Jin Yang, Siwen Xu, Wenhua Xu, Deyu Tang
SSELM-neg: spherical search-based extreme learning machine for drug-target interaction prediction. BMC Bioinform. 24 (1) (2023)
Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn
Pathogen detection in RNA-seq data with Pathonoia. BMC Bioinform. 24 (1) (2023)
Christopher J. Nunn, Eugene Klyshko, Sidhartha Goyal
petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker's yeast. BMC Bioinform. 24 (1) (2023)
Sávio S. Costa, Gislenne da Silva Moia, Artur Silva, Rafael A. Baraúna, Adonney Allan de Oliveira Veras
BADASS: BActeriocin-Diversity ASsessment Software. BMC Bioinform. 24 (1) (2023)
Yifan Zhang, Duc Tran, Tin Nguyen, Sergiu M. Dascalu, Frederick C. Harris
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime. BMC Bioinform. 24 (1) (2023)
Chunhua Liu, Simin Wu, Liying Lai, Jinyu Liu, Zhaofu Guo, Zegen Ye, Xiang Chen
Comprehensive analysis of cuproptosis-related lncRNAs in immune infiltration and prognosis in hepatocellular carcinoma. BMC Bioinform. 24 (1) (2023)
Zicheng Zhang, Xinyue Lin, Shanshan Wu
A hybrid algorithm for clinical decision support in precision medicine based on machine learning. BMC Bioinform. 24 (1) (2023)
Li Guo, Yangyang Xiang, Yuyang Dou, Zibo Yin, Xinru Xu, Lihua Tang, Jiafeng Yu, Jun Wang, Tingming Liang
GBCdb: RNA expression landscapes and ncRNA-mRNA interactions in gallbladder carcinoma. BMC Bioinform. 24 (1) (2023)
Wencan Zhu, Céline Lévy-Leduc, Nils Ternès
Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso. BMC Bioinform. 24 (1) (2023)
Junliang Shang, Xuhui Zhu, Yan Sun, Feng Li, Xiangzhen Kong, Jin-Xing Liu
DM-MOGA: a multi-objective optimization genetic algorithm for identifying disease modules of non-small cell lung cancer. BMC Bioinform. 24 (1) (2023)
Bram van Es, Leon C. Reteig, Sander C. Tan, Marijn Schraagen, Myrthe M. Hemker, Sebastiaan R. S. Arends, Miguel A. R. Rios, Saskia Haitjema
Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods. BMC Bioinform. 24 (1) (2023)
Xiao Liu, Li Teng, Wenqi Zuo, Shixun Zhong, Yuqiao Xu, Jing Sun
Deafness gene screening based on a multilevel cascaded BPNN model. BMC Bioinform. 24 (1) (2023)
Seungjun Ahn, Tyler Grimes, Somnath Datta
A pseudo-value regression approach for differential network analysis of co-expression data. BMC Bioinform. 24 (1) (2023)
Ho Yin Yuen, Jesper Jansson
Normalized L3-based link prediction in protein-protein interaction networks. BMC Bioinform. 24 (1) (2023)
Pawel Pratyush, Suresh Pokharel, Hiroto Saigo, Dukka B. KC
pLMSNOSite: an ensemble-based approach for predicting protein S-nitrosylation sites by integrating supervised word embedding and embedding from pre-trained protein language model. BMC Bioinform. 24 (1) (2023)
Mikhail Gudkov, Loïc Thibaut, Matloob Khushi, Gillian M. Blue, David S. Winlaw, Sally L. Dunwoodie, Eleni Giannoulatou
ConanVarvar: a versatile tool for the detection of large syndromic copy number variation from whole-genome sequencing data. BMC Bioinform. 24 (1) (2023)
Zhengyi Guan, Xiaobing Zhou
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition. BMC Bioinform. 24 (1) (2023)
Maia H. Malonzo, Harri Lähdesmäki
LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model. BMC Bioinform. 24 (1) (2023)
Qun-ting Lin, Wei Yang, Xin Zhang, Qi-gang Li, Yong-feng Liu, Qin Yan, Lei Sun
Systematic and benchmarking studies of pipelines for mammal WGBS data in the novel NGS platform. BMC Bioinform. 24 (1) (2023)
Zequn Zheng, Yongfei Song
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers. BMC Bioinform. 24 (1) (2023)
Zilin Ren, Quan Li, Kajia Cao, Marilyn M. Li, Yunyun Zhou, Kai Wang
Model performance and interpretability of semi-supervised generative adversarial networks to predict oncogenic variants with unlabeled data. BMC Bioinform. 24 (1) (2023)
Dhiego Souto Andrade, Patrick Terrematte, César Rennó-Costa, Alona Zilberberg, Sol Efroni
GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data. BMC Bioinform. 24 (1) (2023)
Seungwon Oh, Sae-Ryung Kang, In-Jae Oh, Min-Soo Kim
Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients. BMC Bioinform. 24 (1) (2023)
Daniyal Rajput, Wei-Jen Wang, Chun-Chuan Chen
Evaluation of a decided sample size in machine learning applications. BMC Bioinform. 24 (1) (2023)
Peijie Zheng, Guiyang Zhang, Yuewu Liu, Guohua Huang
MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction. BMC Bioinform. 24 (1) (2023)
Hai-Ming Feng, Ye Zhao, Wei-Jian Yan, Bin Li
Genomic and immunogenomic analysis of three prognostic signature genes in LUAD. BMC Bioinform. 24 (1) (2023)
Carolina Peixoto, Marta B. Lopes, Marta Martins, Sandra Casimiro, Daniel Sobral, Ana Rita Grosso, Catarina Abreu, Daniela Macedo, Ana Lúcia Costa, Helena Pais, Cecília Alvim, André Mansinho, Pedro Filipe, Pedro Marques da Costa, Afonso Fernandes, Paula Borralho, Cristina Ferreira, João Malaquias, António Quintela, Shannon Kaplan, Mahdi Golkaram, Michael Salmans, Nafeesa Khan, Raakhee Vijayaraghavan, Shile Zhang, Traci Pawlowski, Jim Godsey, Alex So, Li Liu, Luís Costa, Susana Vinga
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization. BMC Bioinform. 24 (1) (2023)
Tony Hauptmann, Stefan Kramer
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction. BMC Bioinform. 24 (1) (2023)
Maria Prager, Daniel Lundin, Fredrik Ronquist, Anders F. Andersson
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. BMC Bioinform. 24 (1) (2023)
Chaozhong Liu, Linhua Wang, Zhandong Liu
Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. BMC Bioinform. 24 (1) (2023)
Yang Ma, Wan-liang Sun, Shuo Shuo Ma, Guanru Zhao, Zhong Liu, Zheng Lu, Dengyong Zhang
LincRNA ZNF529-AS1 inhibits hepatocellular carcinoma via FBXO31 and predicts the prognosis of hepatocellular carcinoma patients. BMC Bioinform. 24 (1) (2023)
Renaud L. M. Tissier, Janne J. M. van Schie, Rob M. F. Wolthuis, Job de Lange, Renée X. de Menezes
ShrinkCRISPR: a flexible method for differential fitness analysis of CRISPR-Cas9 screen data. BMC Bioinform. 24 (1) (2023)
Nand Sharma, Joshua Millstein
CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints. BMC Bioinform. 24 (1) (2023)
Anjana Senanayake, Hasindu Gamaarachchi, Damayanthi Herath, Roshan G. Ragel
DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing. BMC Bioinform. 24 (1) (2023)
Zhong-Hua Chen, Wen-Yuan Zhang, Hui Ye, Yu-Qian Guo, Kai Zhang, Xiang-Ming Fang
A signature of immune-related genes correlating with clinical prognosis and immune microenvironment in sepsis. BMC Bioinform. 24 (1) (2023)
Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery. BMC Bioinform. 24 (1) (2023)