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ORCIDBMC Bioinformatics, Volume 24
Volume 24, Number 1, December 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. 1
- Jianjun Zhang, Xiaoyu Liang
, Samantha Gonzales, Jianguo Liu, Xiaoyi Raymond Gao, Xuexia Wang:
A gene based combination test using GWAS summary data. 2 - Zicheng Zhang, Xinyue Lin, Shanshan Wu:
A hybrid algorithm for clinical decision support in precision medicine based on machine learning. 3 - 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. 4 - Chaozhong Liu, Linhua Wang, Zhandong Liu:
Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. 5 - Maria Prager, Daniel Lundin, Fredrik Ronquist, Anders F. Andersson:
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. 6 - Xuehan Liu, Md Rakibul Hasan, Khandaker Asif Ahmed, Md. Zakir Hossain:
Machine learning to analyse omic-data for COVID-19 diagnosis and prognosis. 7 - Seungjun Ahn, Tyler Grimes, Somnath Datta:
A pseudo-value regression approach for differential network analysis of co-expression data. 8 - Annette Spooner, Gelareh Mohammadi, Perminder S. Sachdev, Henry Brodaty, Arcot Sowmya:
Ensemble feature selection with data-driven thresholding for Alzheimer's disease biomarker discovery. 9 - 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. 10 - 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. 11 - 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. 12 - 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. 13 - Wei Peng, Rong Wu, Wei Dai, Ning Yu:
Identifying cancer driver genes based on multi-view heterogeneous graph convolutional network and self-attention mechanism. 16 - 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. 17 - 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. 18 - Hai-Ming Feng, Ye Zhao, Wei-Jian Yan, Bin Li:
Genomic and immunogenomic analysis of three prognostic signature genes in LUAD. 19 - 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. 20 - 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. 21 - 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. 22 - 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. 23 - Sávio S. Costa, Gislenne da Silva Moia, Artur Silva, Rafael A. Baraúna, Adonney Allan de Oliveira Veras:
BADASS: BActeriocin-Diversity ASsessment Software. 24 - Wencan Zhu, Céline Lévy-Leduc, Nils Ternès:
Identification of prognostic and predictive biomarkers in high-dimensional data with PPLasso. 25 - Anjana Senanayake, Hasindu Gamaarachchi, Damayanthi Herath, Roshan G. Ragel:
DeepSelectNet: deep neural network based selective sequencing for oxford nanopore sequencing. 31 - 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. 32 - 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. 33 - 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. 34 - 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. 35 - 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. 36 - Yidong Zhu, Jun He, Zihua Li, Wenzhong Yang:
Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia. 37 - 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. 38 - 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. 39 - Jiaxing Chen, Yen Kaow Ng, Lu Lin, Xianglilan Zhang, Shuaicheng Li:
On triangle inequalities of correlation-based distances for gene expression profiles. 40 - 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. 41 - Zhengyi Guan, Xiaobing Zhou:
A prefix and attention map discrimination fusion guided attention for biomedical named entity recognition. 42 - 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. 43 - 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. 44 - Tony Hauptmann, Stefan Kramer:
A fair experimental comparison of neural network architectures for latent representations of multi-omics for drug response prediction. 45 - Nand Sharma, Joshua Millstein:
CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints. 46 - Shiva Afshar, Patricia R. Braun, Shizhong Han, Ying Lin:
A multimodal deep learning model to infer cell-type-specific functional gene networks. 47 - Daniyal Rajput, Wei-Jen Wang, Chun-Chuan Chen:
Evaluation of a decided sample size in machine learning applications. 48 - 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. 49 - Christopher J. Nunn, Eugene Klyshko, Sidhartha Goyal:
petiteFinder: an automated computer vision tool to compute Petite colony frequencies in baker's yeast. 50 - Zequn Zheng, Yongfei Song:
Integrated analysis of the voltage-gated potassium channel-associated gene KCNH2 across cancers. 51 - S. Morteza Hashemi, Arash Zabihian, Mohsen Hooshmand, Sajjad Gharaghani:
DRaW: prediction of COVID-19 antivirals by deep learning - an objection on using matrix factorization. 52 - Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn:
Pathogen detection in RNA-seq data with Pathonoia. 53 - 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. 54 - Yifan Zhang, Duc Tran, Tin Nguyen, Sergiu M. Dascalu, Frederick C. Harris Jr.:
A robust and accurate single-cell data trajectory inference method using ensemble pseudotime. 55 - Xiao Liu, Li Teng, Wenqi Zuo, Shixun Zhong, Yuqiao Xu, Jing Sun:
Deafness gene screening based on a multilevel cascaded BPNN model. 56 - 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. 57 - Maia H. Malonzo, Harri Lähdesmäki:
LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model. 58 - Ho Yin Yuen, Jesper Jansson:
Normalized L3-based link prediction in protein-protein interaction networks. 59 - Malik Yousef, Fatma Ozdemir, Amhar Jaber, Jens Allmer, Burcu Bakir-Gungor:
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. 60 - Elie-Julien El Hachem, Nataliya Sokolovska, Hédi Soula:
Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework. 61 - Sungyoung Lee, Choong-Hyun Sun, Heejun Jang, Daeyoon Kim, Sung-Soo Yoon, Youngil Koh, Seung Chan Na, Sung Im Cho, Man Jin Kim, Moon-Woo Seong, Ja Min Byun, Hongseok Yun:
ITDetect: a method to detect internal tandem duplication of FMS-like tyrosine kinase (FLT3) from next-generation sequencing data with high sensitivity and clinical application. 62 - Babak Beikzadeh:
Immunoinformatics design of multi-epitope vaccine using OmpA, OmpD and enterotoxin against non-typhoidal salmonellosis. 63 - Adam B. Olshen, Mark R. Segal:
Does multi-way, long-range chromatin contact data advance 3D genome reconstruction? 64 - Hamid Motamedi, Marzie Mahdizade Ari, Mohsen Shahlaei, Sajad Moradi, Parisa Farhadikia, Amirhoushang Alvandi, Ramin Abiri:
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. 65 - Jae Yong Ryu, Woo Dae Jang, Jidon Jang, Kwang-Seok Oh:
PredAOT: a computational framework for prediction of acute oral toxicity based on multiple random forest models. 66 - Mona Shafaghi, Zohreh Bahadori, Hamid Madanchi, Mohammad Mehdi Ranjbar, Ali Akbar Shabani, Seyed Fazlollah Mousavi:
Immunoinformatics-aided design of a new multi-epitope vaccine adjuvanted with domain 4 of pneumolysin against Streptococcus pneumoniae strains. 67 - Kai Chen, Xiaodong Zhu, Jiahao Wang, Lei Hao, Zhen Liu, Yuanning Liu:
ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction. 68 - Antonio Benítez-Hidalgo, José Francisco Aldana Montes, Ismael Navas-Delgado, María del Mar Roldán García:
SALON ontology for the formal description of sequence alignments. 69 - Nika Abdollahi, Lucile Jeusset, Anne Langlois De Septenville, Frédéric Davi, Juliana S. Bernardes:
Reconstructing B cell lineage trees with minimum spanning tree and genotype abundances. 70 - Jonathan Tellechea-Luzardo, Hèctor Martín Lázaro, Raúl Moreno López, Pablo Carbonell:
Sensbio: an online server for biosensor design. 71 - Xiangjun Ji, Junwei Cai, Lixin Liang, Tieliu Shi, Jinghua Liu:
Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages. 72 - Koen Swaerts, Franceska Dedeurwaerdere, Dieter De Smet, Peter De Jaeger, Geert A. Martens:
DeltaMSI: artificial intelligence-based modeling of microsatellite instability scoring on next-generation sequencing data. 73 - Arianna I. Krinos, Natalie R. Cohen, Michael J. Follows, Harriet Alexander:
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. 74 - Yusra A. Ameen, Dalia M. Badary, Ahmad Elbadry I. Abonnoor, Khaled F. Hussain, Adel A. Sewisy:
Which data subset should be augmented for deep learning? a simulation study using urothelial cell carcinoma histopathology images. 75 - Rui Chen, Jun-Min Wei:
Integrated analysis identifies oxidative stress-related lncRNAs associated with progression and prognosis in colorectal cancer. 76 - Lacey W. Heinsberg, Daniel E. Weeks:
dbGaPCheckup: pre-submission checks of dbGaP-formatted subject phenotype files. 77 - Erik Huckvale, Hunter N. B. Moseley:
kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes. 78 - Zhijian Li, Chao-Chung Kuo, Fabio Ticconi, Mina Shaigan, Julia Gehrmann, Eduardo G. Gusmão, Manuel Allhoff, Martin Manolov, Martin Zenke, Ivan G. Costa:
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. 79 - Runtian Gao, Junwei Luo, Hongyu Ding, Haixia Zhai:
INSnet: a method for detecting insertions based on deep learning network. 80 - Saiyidan Yalimaimaiti, Xiaoqiao Liang, Haili Zhao, Hong Dou, Wei Liu, Ying Yang, Li Ning:
Establishment of a prognostic signature for lung adenocarcinoma using cuproptosis-related lncRNAs. 81 - Malu Luz Calle, Meritxell Pujolassos, Antonio Susín:
coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies. 82 - Aleksandr Kotov, Andrei Zinovyev, Anne-Helene Monsoro-Burq:
scEvoNet: a gradient boosting-based method for prediction of cell state evolution. 83 - Lior I. Shachaf, Elijah Roberts, Patrick Cahan, Jie Xiao:
Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM. 84 - Shaoming Pan, Xin Liu, Ningdi Xie, Yanwen Chong:
EG-TransUNet: a transformer-based U-Net with enhanced and guided models for biomedical image segmentation. 85 - Patrick M. Carry, Tim Vigers, Lauren A. Vanderlinden, Carson Keeter, Fran Dong, Teresa Buckner, Elizabeth Litkowski, Ivana Yang, Jill M. Norris, Katherina J. Kechris:
Propensity scores as a novel method to guide sample allocation and minimize batch effects during the design of high throughput experiments. 86 - Katherine F. Steward, Mohammed Refai, William E. Dyer, Valérie Copié, Jennifer Lachowiec, Brian Bothner:
Acute stress reduces population-level metabolic and proteomic variation. 87 - Mirjam Figaschewski, Bilge Sürün, Thorsten Tiede, Oliver Kohlbacher:
The personalized cancer network explorer (PeCaX) as a visual analytics tool to support molecular tumor boards. 88 - Wan-Xia Yang, Hong-Wei Gao, Jia-Bo Cui, An-An Zhang, Fang-Fang Wang, Jian-Qin Xie, Ming-Hua Lu, Chong-Ge You:
Development and validation of a coagulation-related genes prognostic model for hepatocellular carcinoma. 89 - Petter Mostad, Andreas Tillmar, Daniel Kling:
Improved computations for relationship inference using low-coverage sequencing data. 90 - Fan Chang, Jiang-Hui Zhang, Wen-Song Wu, Shuai Tang, Zheng lv, Fang-Min Chen:
FDC-SP as a diagnostic and prognostic biomarker and modulates immune infiltrates in renal cell carcinoma. 91 - Luísa C. de Souza, Karolayne S. Azevedo, Jackson Gomes de Souza, Raquel de M. Barbosa, Marcelo A. C. Fernandes:
New proposal of viral genome representation applied in the classification of SARS-CoV-2 with deep learning. 92 - Jing Wang, Shuo Zhang, Runzhi Li, Gang Chen, Siyu Yan, Lihong Ma:
Multi-view feature representation and fusion for drug-drug interactions prediction. 93 - Yoonsung Joh, Kangbae Lee, Hyunwoo Kim, Heejin Park:
Progressive search in tandem mass spectrometry. 94 - Nahla AlKurabi, Ahad AlGahtani, Turki M. Sobahy:
CACSV: a computational web-sever that provides classification for cancer somatic genetic variants from different tissues. 95 - Shaima Belhechmi, Gwénaël Le Teuff, Riccardo De Bin, Federico Rotolo, Stefan Michiels:
Favoring the hierarchical constraint in penalized survival models for randomized trials in precision medicine. 96 - Siyu Yang, Peiliang Zhang, Chao Che, Zhaoqian Zhong:
B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism. 97 - Timothy Dunn, David T. Blaauw, Reetuparna Das, Satish Narayanasamy:
nPoRe: n-polymer realigner for improved pileup-based variant calling. 98 - Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi:
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. 99 - Bin Zhao, Fang Fang, Yiqun Liao, Yuji Chen, Fei Wang, Yichao Ma, Chen Wei, Jiahao Zhao, Hao Ji, Daorong Wang, Dong Tang:
Novel m7G-related lncRNA signature for predicting overall survival in patients with gastric cancer. 100 - Yannis Schumann, Julia E. Neumann, Philipp Neumann:
Robust classification using average correlations as features (ACF). 101 - Guanjue Xiang, Belinda Giardine, Lin An, Chen Sun, Cheryl A. Keller, Elisabeth F. Heuston, Stacie M. Anderson, Martha Kirby, David M. Bodine, Yu Zhang, Ross C. Hardison:
Snapshot: a package for clustering and visualizing epigenetic history during cell differentiation. 102 - Zuming Xiong, Wenxin Li, Xiangrong Luo, Yirong Lin, Wei Huang, Sen Zhang:
Seven bacterial response-related genes are biomarkers for colon cancer. 103 - Puyu Liu, Jihang Luo, Na Tan, Chengfang Li, Jieyu Xu, Xiaorong Yang:
Establishing a prognostic model of chromatin modulators and identifying potential drug candidates in renal clear cell patients. 104 - Seokjin Han, Jinhee Hong, So Jeong Yun, Hee Jung Koo, Tae Yong Kim:
PWN: enhanced random walk on a warped network for disease target prioritization. 105 - Kevin M. Shebek, Jonathan Strutz, Linda J. Broadbelt, Keith E. J. Tyo:
Pickaxe: a Python library for the prediction of novel metabolic reactions. 106 - Ivo Henrique Provensi Vieira, Eduardo Buganemi Botelho, Thales Junior de Souza Gomes, Roger Kist, Rafael A. Caceres, Fernando Berton Zanchi:
Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS. 107 - Xu Zhang, Ya Su, Andrew N. Lane, Arnold J. Stromberg, Teresa W.-M. Fan, Chi Wang:
Bayesian kinetic modeling for tracer-based metabolomic data. 108 - Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nihad Alajez, Tanvir Alam:
MSLP: mRNA subcellular localization predictor based on machine learning techniques. 109
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