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BMC Bioinformatics, Volume 24
Volume 24, Number 1, December 2023
- Yauheniya Zhdanovich, Jörg Ackermann, Peter J. Wild, Jens Köllermann, Katrin Bankov
, Claudia Döring
Evaluation of automatic discrimination between benign and malignant prostate tissue in the era of high precision digital pathology. 1 - Jianjun Zhang, Xiaoyu Liang
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
ASV portal: an interface to DNA-based biodiversity data in the Living Atlas. 6 - Xuehan Liu, Md. Rakibul Hasan
Machine learning to analyse omic-data for COVID-19 diagnosis and prognosis. 7 - Seungjun Ahn
A pseudo-value regression approach for differential network analysis of co-expression data. 8 - Annette Spooner
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
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
Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization. 17 - Ping Zhang
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
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
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
BADASS: BActeriocin-Diversity ASsessment Software. 24 - Wencan Zhu
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
GENTLE: a novel bioinformatics tool for generating features and building classifiers from T cell repertoire cancer data. 32 - Qun-ting Lin, Wei Yang
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
Cuproptosis-related lncRNA signature for prognostic prediction in patients with acute myeloid leukemia. 37 - Lingzhi Hu, Chengzhou Fu, Zhonglu Ren
SSELM-neg: spherical search-based extreme learning machine for drug-target interaction prediction. 38 - Seungwon Oh, Sae-Ryung Kang, In-Jae Oh
Deep learning model integrating positron emission tomography and clinical data for prognosis prediction in non-small cell lung cancer patients. 39 - Jiaxing Chen
On triangle inequalities of correlation-based distances for gene expression profiles. 40 - Pawel Pratyush
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
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
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
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
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
PriPath: identifying dysregulated pathways from differential gene expression via grouping, scoring, and modeling with an embedded feature selection approach. 60 - Elie-Julien El Hachem
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
Designing multi-epitope vaccine against important colorectal cancer (CRC) associated pathogens based on immunoinformatics approach. 65 - Jae Yong Ryu, Woo Dae Jang, Jidon Jang
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
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
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
Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. 74 - Yusra A. Ameen
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
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
RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data. 79 - Runtian Gao
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
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
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
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
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
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
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
B-LBConA: a medical entity disambiguation model based on Bio-LinkBERT and context-aware mechanism. 97 - Timothy Dunn
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
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
Robust classification using average correlations as features (ACF). 101 - Guanjue Xiang
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
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 - Zihao Yang, Kuiyuan Tong, Shiyu Jin, Shiyan Wang, Chao Yang, Feng Jiang:
CNN-Siam: multimodal siamese CNN-based deep learning approach for drug‒drug interaction prediction. 110 - Ranze Xie, Xiangzhen Zan, Ling Chu, Yanqing Su, Peng Xu, Wenbin Liu:
Study of the error correction capability of multiple sequence alignment algorithm (MAFFT) in DNA storage. 111 - Mpho Mokoatle, Vukosi Marivate, Darlington S. Mapiye, Riana Bornman, Vanessa M. Hayes
A review and comparative study of cancer detection using machine learning: SBERT and SimCSE application. 112 - Xuping Xie, Yan Wang, Kai He, Nan Sheng
Predicting miRNA-disease associations based on PPMI and attention network. 113 - Bingran Shen, Gloria M. Coruzzi, Dennis E. Shasha:
EnsInfer: a simple ensemble approach to network inference outperforms any single method. 114 - Dario Tommasini
multiWGCNA: an R package for deep mining gene co-expression networks in multi-trait expression data. 115 - Scott D. Brown, Lisa Dreolini, Jessica F. Wilson, Miruna Balasundaram, Robert A. Holt
Complete sequence verification of plasmid DNA using the Oxford Nanopore Technologies' MinION device. 116 - Christiam Camacho
ElasticBLAST: accelerating sequence search via cloud computing. 117 - Canxuan Li, Weibin Xie:
Identification and validation of tumor-infiltrating lymphocyte-related prognosis signature for predicting prognosis and immunotherapeutic response in bladder cancer. 118 - Huidong Ma, Cheng Zhong, Danyang Chen, Haofa He, Feng Yang:
cnnLSV: detecting structural variants by encoding long-read alignment information and convolutional neural network. 119 - Léo Bürgy, Martin Weigert, Georgios Hatzopoulos
CenFind: a deep-learning pipeline for efficient centriole detection in microscopy datasets. 120 - Yeremia Gunawan Adhisantoso
GVC: efficient random access compression for gene sequence variations. 121 - Chun-Chi Chen, Yi-Ming Chan:
REDfold: accurate RNA secondary structure prediction using residual encoder-decoder network. 122 - Chaozhong Liu, Linhua Wang, Zhandong Liu
Correction: Single-cell multi-omics integration for unpaired data by a siamese network with graph-based contrastive loss. 123 - Changbeom Shim
CellTrackVis: interactive browser-based visualization for analyzing cell trajectories and lineages. 124 - Jose Laborde, Paul A. Stewart, Zhihua Chen, Yian A. Chen, Naomi C. Brownstein
Sparse clusterability: testing for cluster structure in high dimensions. 125 - K. Syama
Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE. 126 - Abdullah Karaaslanli, Satabdi Saha, Tapabrata Maiti, Selin Aviyente:
Kernelized multiview signed graph learning for single-cell RNA sequencing data. 127 - Cong Ji
Shine: A novel strategy to extract specific, sensitive and well-conserved biomarkers from massive microbial genomic datasets. 128 - Yu Sun, Hongwei Wu, Zhengrong Xu, Zhenyu Yue, Ke Li:
Prediction of hot spots in protein-DNA binding interfaces based on discrete wavelet transform and wavelet packet transform. 129 - Wei Li, Yuhuan Chi, Kun Yu, Weidong Xie
A two-stage hybrid biomarker selection method based on ensemble filter and binary differential evolution incorporating binary African vultures optimization. 130 - Christoffer Trier Maansson
DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies. 131 - Rishab Jain
ICOR: improving codon optimization with recurrent neural networks. 132 - Timothy R. Fallon, Tereza Calounová, Martin Mokrejs, Jing-Ke Weng, Tomás Pluskal
transXpress: a Snakemake pipeline for streamlined de novo transcriptome assembly and annotation. 133 - Maija Utriainen, John H. Morris:
clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape. 134 - Elena Solovieva
PSReliP: an integrated pipeline for analysis and visualization of population structure and relatedness based on genome-wide genetic variant data. 135 - Vandana Sreedharan, Upinder S. Bhalla, Naren Ramakrishnan:
Using sensitivity analyses to understand bistable system behavior. 136 - Yu Chen, Lixin Gao, Tianjiao Zhang
Stack-VTP: prediction of vesicle transport proteins based on stacked ensemble classifier and evolutionary information. 137 - Jin Du
Automatic block-wise genotype-phenotype association detection based on hidden Markov model. 138 - Zixuan Wang, Yi Zhou
Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data. 139 - Negar Hossein-Nezhad Daneshvar, Yosef Masoudi-Sobhanzadeh, Yadollah Omidi:
A voting-based machine learning approach for classifying biological and clinical datasets. 140 - Pooja Arora
iIL13Pred: improved prediction of IL-13 inducing peptides using popular machine learning classifiers. 141 - Junjie Zhang, Guoli Ji, Xilin Gao, Jinting Guan
Single-nucleus gene and gene set expression-based similarity network fusion identifies autism molecular subtypes. 142 - Pasquale Claudio Africa
lifex-fiber: an open tool for myofibers generation in cardiac computational models. 143 - Behrouz Bokharaeian, Mohammad Dehghani, Alberto Díaz
Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method. 144 - James F. Fleming, Torsten H. Struck:
nRCFV: a new, dataset-size-independent metric to quantify compositional heterogeneity in nucleotide and amino acid datasets. 145 - Ruowen Li, Wenjie Qu, Qingqing Liu, Yilin Tan, Wenjing Zhang, Yiping Hao, Nan Jiang, Zhonghao Mao, Jinwen Ye, Jun Jiao, Qun Gao, Baoxia Cui, Taotao Dong:
Development and validation of a deep learning survival model for cervical adenocarcinoma patients. 146 - Airexiati Tuhongjiang, Feng Wang, Chengrong Zhang, Sisi Pang, Yujiang Qu, Bo Feng, Gulimire Amuti:
Construction of an RNA modification-related gene predictive model associated with prognosis and immunity in gastric cancer. 147 - Rajnish Kumar, Rajkrishna Mondal, Tapobrata Lahiri, Manoj Kumar Pal:
Application of sequence semantic and integrated cellular geography approach to study alternative biogenesis of exonic circular RNA. 148 - Kui Fan, Bo-hui Zhang, Deng Han, Yun-chuan Sun:
EZH2 as a prognostic-related biomarker in lung adenocarcinoma correlating with cell cycle and immune infiltrates. 149 - Kristina Lietz, Babak Saremi, Lena Wiese
Genealyzer: web application for the analysis and comparison of gene expression data. 150 - Peng Chen, Haoran Zheng:
Drug-target interaction prediction based on spatial consistency constraint and graph convolutional autoencoder. 151 - Pengli Cai, Sheng Liu
SynBioTools: a one-stop facility for searching and selecting synthetic biology tools. 152 - Wei Zhao, Qamar Raza Qadri, Zhenyang Zhang, Zhen Wang, Yuchun Pan, Qishan Wang
PyAGH: a python package to fast construct kinship matrices based on different levels of omic data. 153 - Layla Hosseini-Gerami, Ixavier Alonzo Higgins, David A. Collier, Emma Laing, David Evans, Howard Broughton, Andreas Bender:
Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis. 154 - He Li
Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis. 155 - Saleh Musleh, Mohammad Tariqul Islam, Rizwan Qureshi, Nihad Alajez, Tanvir Alam:
Correction: MSLP: mRNA subcellular localization predictor based on machine learning techniques. 156 - Chun-Ling Lin, Kun-Chi Wu:
Development of revised ResNet-50 for diabetic retinopathy detection. 157 - Marc Vaisband, Maria Schubert, Franz Josef Gassner, Roland Geisberger, Richard Greil, Nadja Zaborsky, Jan Hasenauer:
Validation of genetic variants from NGS data using deep convolutional neural networks. 158 - Marco Alvarado Cano, Ginger Tsueng
Schema Playground: a tool for authoring, extending, and using metadata schemas to improve FAIRness of biomedical data. 159 - Golam Md Mortuza, Jorge Guerrero, Shoshanna Llewellyn, Michael D. Tobiason, George D. Dickinson, William L. Hughes, Reza Zadegan, Tim Andersen
In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA). 160 - Leiv Rønneberg, Paul D. W. Kirk, Manuela Zucknick:
Dose-response prediction for in-vitro drug combination datasets: a probabilistic approach. 161 - Linlin Zhang, Dianrong Lu, Xuehua Bi, Kai Zhao, Guanglei Yu, Na Quan:
Predicting disease genes based on multi-head attention fusion. 162 - Qian Wang, Maozu Guo, Jian Chen, Ran Duan:
A gene regulatory network inference model based on pseudo-siamese network. 163 - Steven A. Eschrich, Xiaoqing Yu, Jamie K. Teer
Fast all versus all genotype comparison using DNA/RNA sequencing data: method and workflow. 164 - William Breslin, Doan Pham:
Machine learning and drug discovery for neglected tropical diseases. 165 - Ksenia Zlobina
Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data. 166 - Ho-min Park
CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins. 167 - Joung Min Choi
meth-SemiCancer: a cancer subtype classification framework via semi-supervised learning utilizing DNA methylation profiles. 168 - Joung Min Choi
moBRCA-net: a breast cancer subtype classification framework based on multi-omics attention neural networks. 169 - Jitong Cai, Jianan Zhan, Dan E. Arking, Joel S. Bader
Priors, population sizes, and power in genome-wide hypothesis tests. 170 - Muhammad Asif, Hugo F. M. C. Martiniano, Andre Lamurias
DGH-GO: dissecting the genetic heterogeneity of complex diseases using gene ontology. 171 - Mirrelijn M. van Nee
ecpc: an R-package for generic co-data models for high-dimensional prediction. 172 - Lin Chen
Magicmol: a light-weighted pipeline for drug-like molecule evolution and quick chemical space exploration. 173 - Mustafa Siddiqui, Gavin C. Conant
POInTbrowse: orthology prediction and synteny exploration for paleopolyploid genomes. 174 - Hui Zhang, Weiyang Chen:
Automated recognition and analysis of body bending behavior in C. elegans. 175 - Tong Wu, Na Li, Fengyuan Luo, Zhihong Chen, Liyuan Ma, Tao Hu, Guini Hong, Hongdong Li:
Screening prognostic markers for hepatocellular carcinoma based on pyroptosis-related lncRNA pairs. 176 - Changlong Gu, Xiaoying Li:
Prediction of disease-related miRNAs by voting with multiple classifiers. 177 - Trevor Doherty, Emma Dempster, Eilis J. Hannon, Jonathan Mill
A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator. 178 - Nassim Versbraegen, Barbara Gravel, Charlotte Nachtegael
Faster and more accurate pathogenic combination predictions with VarCoPP2.0. 179 - Jinghan Yang
ERStruct: a fast Python package for inferring the number of top principal components from whole genome sequencing data. 180 - Matthias van den Belt, Cameron L. M. Gilchrist, Thomas J. Booth, Yit-Heng Chooi
CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters. 181 - Michael Olbrich
MBECS: Microbiome Batch Effects Correction Suite. 182 - Youjin Kim, Junseok Kwon:
AttSec: protein secondary structure prediction by capturing local patterns from attention map. 183 - Yangyang Xie, Xue Song, Danwei Du, Zhongkai Ni, Hai Huang:
Identification of cuproptosis-related lncRNAs to predict prognosis and immune infiltration characteristics in alimentary tract malignancies. 184 - Arianna I. Krinos
Correction: Reverse engineering environmental metatranscriptomes clarifies best practices for eukaryotic assembly. 185 - Raphaël Mourad:
Semi-supervised learning improves regulatory sequence prediction with unlabeled sequences. 186 - Marta Pelizzola
Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization. 187 - Leon Wong, Lei Wang, Zhu-Hong You, Chang-An Yuan, Yu-An Huang
GKLOMLI: a link prediction model for inferring miRNA-lncRNA interactions by using Gaussian kernel-based method on network profile and linear optimization algorithm. 188 - Yue Shen
HLA-Clus: HLA class I clustering based on 3D structure. 189 - Seung Min Baik
Deep learning approach for early prediction of COVID-19 mortality using chest X-ray and electronic health records. 190 - YaLing Liu, Dan Li, Yong Chen, YiJuan Liu, YiJuan Lin, XunRu Huang, Ting Wu, ChengDang Wang
Integrated bioinformatics analysis for conducting a prognostic model and identifying immunotherapeutic targets in gastric cancer. 191 - Chunxun Liu, Zhaowei Qu, Haoran Zhao, Peng Wang, Chao Zhan, Yubao Zhang:
Pan-cancer analysis of SYNGR2 with a focus on clinical implications and immune landscape in liver hepatocellular carcinoma. 192 - Jing Huang, Yuting Zhou, Haoran Zhang, Yiming Wu:
A neural network model to screen feature genes for pancreatic cancer. 193 - Jacob Williams, Shuangshuang Xu
BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies. 194 - Peter Y. Wang
A statistical approach for identifying primary substrates of ZSWIM8-mediated microRNA degradation in small-RNA sequencing data. 195 - Li Rao
Nonnegative matrix factorization analysis and multiple machine learning methods identified IL17C and ACOXL as novel diagnostic biomarkers for atherosclerosis. 196 - Nae-Chyun Chen, Alexey Kolesnikov, Sidharth Goel, Taedong Yun
Improving variant calling using population data and deep learning. 197 - Magdalena Wysocka, Oskar Wysocki
A systematic review of biologically-informed deep learning models for cancer: fundamental trends for encoding and interpreting oncology data. 198 - Renliang Zhang, Guanqing Jia, Xianmin Diao:
geneHapR: an R package for gene haplotypic statistics and visualization. 199 - Sébastien Ouellet
CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides. 200 - Ping Zhang, Min Wang, Tao Zhou
SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis. 201 - E. Amiri Souri, A. Chenoweth, S. N. Karagiannis
Drug repurposing and prediction of multiple interaction types via graph embedding. 202 - Peiqiang Liu, Chang Liu, Yanyan Mao, Junhong Guo, Fanshu Liu, Wangmin Cai, Feng Zhao:
Identification of essential proteins based on edge features and the fusion of multiple-source biological information. 203 - Thomas M. Adams
HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes. 204 - Fedor Sharko
CircPrime: a web-based platform for design of specific circular RNA primers. 205 - Yuya Hatano
Accuracy of a machine learning method based on structural and locational information from AlphaFold2 for predicting the pathogenicity of TARDBP and FUS gene variants in ALS. 206 - Chloe Engler Hart, Daniel Ence, David Healey, Daniel Domingo-Fernández:
On the correspondence between the transcriptomic response of a compound and its effects on its targets. 207 - Damian J. Magill, Timofey A. Skvortsov
DePolymerase Predictor (DePP): a machine learning tool for the targeted identification of phage depolymerases. 208 - Budi Permana
GraphSNP: an interactive distance viewer for investigating outbreaks and transmission networks using a graph approach. 209 - Darren A. V. Scott
Bayesian compositional regression with microbiome features via variational inference. 210 - Jingli Wu, Qinghua Nie, Gaoshi Li, Kai Zhu:
Identifying driver pathways based on a parameter-free model and a partheno-genetic algorithm. 211 - Georgios Argyris, Alberto Lluch-Lafuente
Reducing Boolean networks with backward equivalence. 212 - Yan Zheng, Xuequn Shang:
SVcnn: an accurate deep learning-based method for detecting structural variation based on long-read data. 213 - Yunze Liu
Empowering biologists to decode omics data: the Genekitr R package and web server. 214 - Belinda B. Garana, James H. Joly, Alireza Delfarah, Hyunjun Hong, Nicholas A. Graham:
Drug mechanism enrichment analysis improves prioritization of therapeutics for repurposing. 215 - Xu Chen, Chuang Peng, Yu Chen, Bai Ding, Sulai Liu, Yinghui Song, Yuhang Li, Bo Sun, Ranzhiqiang Yang:
A T-cell-related signature for prognostic stratification and immunotherapy response in hepatocellular carcinoma based on transcriptomics and single-cell sequencing. 216 - Zile Wang
scSemiAAE: a semi-supervised clustering model for single-cell RNA-seq data. 217 - Xiaoyu Yu:
Genofunc: genome annotation and identification of genome features for automated pipelining analysis of virus whole genome sequences. 218 - Huancheng Fu, Ce Shan, Fanchen Kang, Ling Yu, Zhonghan Li, Yike Yin
CRISPR-GRANT: a cross-platform graphical analysis tool for high-throughput CRISPR-based genome editing evaluation. 219 - Chao Cao
CircSSNN: circRNA-binding site prediction via sequence self-attention neural networks with pre-normalization. 220 - Kyle A. O'Connell, Zelaikha B. Yosufzai, Ross Campbell, Collin J. Lobb, Haley T. Engelken, Laura M. Gorrell, Thad B. Carlson, Josh J. Catana, Dina Mikdadi, Vivien R. Bonazzi, Juergen A. Klenk:
Accelerating genomic workflows using NVIDIA Parabricks. 221 - Xusheng Zhang, Yongxin Ma, Kejun Liu, Long Chen, Lin Ding, Weihu Ma, Bendong Chen:
Risk prediction for dermatomyositis-associated hepatocellular carcinoma. 222 - Bingye Shi, Wei Zhang, Tao Wang, Zhenyu Cui:
The therapeutic and prognostic role of cuproptosis-related genes in triple negative breast cancer. 223 - Hongfang Zhou, Yinbo Xin, Suli Li:
A diabetes prediction model based on Boruta feature selection and ensemble learning. 224 - Guihua Tang, Jianqiao Peng, Longwei Huo, Wen Yin:
An N6-methyladenosine regulation- and mRNAsi-related prognostic index reveals the distinct immune microenvironment and immunotherapy responses in lower-grade glioma. 225 - Qiaonan Duan, Weiyi Wang, Feiling Feng, Xiaoqing Jiang, Hao Chen, Dadong Zhang, Tongyi Zhang:
Comut-viz: efficiently creating and browsing comutation plots online. 226 - Arnaud Ferré, Philippe Langlais:
An analysis of entity normalization evaluation biases in specialized domains. 227 - Luca Del Core
A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies. 228 - Min Chen, Yingwei Deng, Zejun Li, Yifan Ye, Ziyi He:
KATZNCP: a miRNA-disease association prediction model integrating KATZ algorithm and network consistency projection. 229 - Bruno Moretti
Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers. 230 - Giulia Russo, Elena Crispino, Avisa Maleki, Valentina Di Salvatore, Filippo Stanco, Francesco Pappalardo
Beyond the state of the art of reverse vaccinology: predicting vaccine efficacy with the universal immune system simulator for influenza. 231 - Chaoran Chen
LAPIS is a fast web API for massive open virus sequencing data. 232 - Shuya Nakata
End-to-end protein-ligand complex structure generation with diffusion-based generative models. 233 - Hua Zhong, Jing Luo, Lin Tang, Shicheng Liao, Zhonghao Lu, Guoliang Lin, Robert W. Murphy, Lin Liu:
Association filtering and generative adversarial networks for predicting lncRNA-associated disease. 234 - Lisa Fiedler, Matthias Bernt
Detecting gene breakpoints in noisy genome sequences using position-annotated colored de-Bruijn graphs. 235 - Patrick Kunzmann
Biotite: new tools for a versatile Python bioinformatics library. 236 - Øystein Øvrebø, Miina Ojansivu, Kimmo Kartasalo
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy. 237 - Liang Chen, Yiming Weng, Xue Cui, Qian Li, Min Peng, Qibin Song:
Comprehensive analyses of a CD8+ T cell infiltration related gene signature with regard to the prediction of prognosis and immunotherapy response in lung squamous cell carcinoma. 238 - Jeff Jones, Elliot J. MacKrell, Ting-Yu Wang, Brett Lomenick, Michael L. Roukes, Tsui-Fen Chou:
Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization. 239 - Gabriel Bianchin de Oliveira, Hélio Pedrini, Zanoni Dias:
TEMPROT: protein function annotation using transformers embeddings and homology search. 242 - Rohan S. Mehta, Robert Petit, Timothy D. Read, Daniel B. Weissman:
Detecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes. 243 - Michael L. Sierk
3DVizSNP: a tool for rapidly visualizing missense mutations identified in high throughput experiments in iCn3D. 244 - Huangchao Xu, Baohua Zhang, Qian Liu:
Deep learning-based classification model for GPR151 activator activity prediction. 245 - Willow Carretero Chavez
kboolnet: a toolkit for the verification, validation, and visualization of reaction-contingency (rxncon) models. 246 - Carlos J. Rivera-Rivera
CastNet: a systems-level sequence evolution simulator. 247 - Jin Xu:
SBMLKinetics: a tool for annotation-independent classification of reaction kinetics for SBML models. 248 - Shenghao Cao
RegCloser: a robust regression approach to closing genome gaps. 249 - Najeha R. Anwardeen
Statistical methods and resources for biomarker discovery using metabolomics. 250 - Khyber Shinwari
In-silico assessment of high-risk non-synonymous SNPs in ADAMTS3 gene associated with Hennekam syndrome and their impact on protein stability and function. 251 - Tomoya Mori, Toshiro Takase, Kuan-Chun Lan
eSPRESSO: topological clustering of single-cell transcriptomics data to reveal informative genes for spatio-temporal architectures of cells. 252 - Lei Wang, Han Cao, Liu Yuan, Xiaoxu Guo, Yachao Cui:
Child-Sum EATree-LSTMs: enhanced attentive Child-Sum Tree-LSTMs for biomedical event extraction. 253 - Koki Tsuyuzaki, Kentaro Yamamoto, Yu Toyoshima, Hirofumi Sato, Manami Kanamori, Takayuki Teramoto, Takeshi Ishihara, Yuichi Iino, Itoshi Nikaido:
WormTensor: a clustering method for time-series whole-brain activity data from C. elegans. 254 - Yuqi Song, Jianzun Ma, Linan Fang, Mingbo Tang, Xinliang Gao, Dongshan Zhu, Wei Liu:
Endoplasmic reticulum stress-related gene model predicts prognosis and guides therapies in lung adenocarcinoma. 255 - Yue Pan
The Poisson distribution model fits UMI-based single-cell RNA-sequencing data. 256 - Weiwei Qian, Jian Zhou, Songtao Shou:
Exploration of m6A methylation regulators as epigenetic targets for immunotherapy in advanced sepsis. 257 - Cansu Alakus, Denis Larocque, Aurélie Labbe:
Covariance regression with random forests. 258 - Ashna Dhingra
A MATLAB-based app to improve LC-MS/MS data analysis for N-linked glycan peak identification. 259 - Chengxin Zhang:
BeEM: fast and faithful conversion of mmCIF format structure files to PDB format. 260 - Yongxian Fan, Hui Xiong, Guicong Sun:
DeepASDPred: a CNN-LSTM-based deep learning method for Autism spectrum disorders risk RNA identification. 261 - Aysam Guerler
Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy. 263 - Jiayao Zhang, Chunling Hu, Qianqian Zhang:
Gene regulatory network inference based on a nonhomogeneous dynamic Bayesian network model with an improved Markov Monte Carlo sampling. 264 - Iakes Goenaga, Edgar Andrés, Koldo Gojenola, Aitziber Atutxa
Advances in monolingual and crosslingual automatic disability annotation in Spanish. 265 - Alyssa N. Obermayer, Darwin Chang, Gabrielle Nobles, Mingxiang Teng
PATH-SURVEYOR: pathway level survival enquiry for immuno-oncology and drug repurposing. 266 - Yaru Hao, Xiao-Yuan Jing, Qixing Sun:
Cancer survival prediction by learning comprehensive deep feature representation for multiple types of genetic data. 267 - Thorhildur Juliusdottir:
topr: an R package for viewing and annotating genetic association results. 268 - Yunbin Shi, Juntao Huang, Yi Hu, Yi Shen:
Multiomics data analyses to identify SLC25A17 as a novel biomarker to predict the prognosis and immune microenvironment in head and neck squamous cell carcinoma. 269 - Xue-Qin Chen
Comprehensive analysis of KLF2 as a prognostic biomarker associated with fibrosis and immune infiltration in advanced hepatocellular carcinoma. 270 - Cédric Beaulac, Sidi Wu, Erin Gibson, Michelle F. Miranda
Neuroimaging feature extraction using a neural network classifier for imaging genetics. 271 - Fotis Aisopos, Georgios Paliouras:
Comparing methods for drug-gene interaction prediction on the biomedical literature knowledge graph: performance versus explainability. 272 - Fareed Ahmad, Muhammad Usman Ghani Khan, Ahsen Tahir, Farhan Masud:
Deep ensemble approach for pathogen classification in large-scale images using patch-based training and hyper-parameter optimization. 273 - Ran Li, Haiyan Chen, Chaoxi Li, Yiwei Qi, Kai Zhao, Junwen Wang, Chao You, Haohao Huang:
The prognostic value and immune landscaps of m6A/m5C-related lncRNAs signature in the low grade glioma. 274 - Roohallah Mahdi-Esferizi, Behnaz Haji Molla Hoseyni, Amir Mehrpanah, Yazdan Golzade, Ali Najafi
DeeP4med: deep learning for P4 medicine to predict normal and cancer transcriptome in multiple human tissues. 275 - Oguz C. Binatli, Mehmet Gönen:
MOKPE: drug-target interaction prediction via manifold optimization based kernel preserving embedding. 276 - Samuel Boyd, Chad Slawson, Jeffrey A. Thompson
AMEND: active module identification using experimental data and network diffusion. 277 - Yuanyuan Zhang, Yinfei Feng, Mengjie Wu, Zengqian Deng, Shudong Wang:
VGAEDTI: drug-target interaction prediction based on variational inference and graph autoencoder. 278 - Gideon Klaila
Supervised topological data analysis for MALDI mass spectrometry imaging applications. 279 - Li Fu, Qun Huang, Yongfeng Wu, Diang Chen:
Prognostic analysis of uveal melanoma based on the characteristic genes of M2-type macrophages in the tumor microenvironment. 280 - Junyao Kuang, Kristin Michel
GeCoNet-Tool: a software package for gene co-expression network construction and analysis. 281 - Mitja Briscik
Improvement of variables interpretability in kernel PCA. 282 - Marilyn Gatica
VolumePeeler: a novel FIJI plugin for geometric tissue peeling to improve visualization and quantification of 3D image stacks. 283 - Anne Guichard
MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. 284 - Yanwen Chong, Ningdi Xie, Xin Liu, Shaoming Pan:
P-TransUNet: an improved parallel network for medical image segmentation. 285 - Aimin Yan, Cristina Baricordi, Quoc Nguyen, Luigi Barbarossa, Mariana Loperfido, Luca Biasco
IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods. 286 - Kobe Janssen, Ramon Duran-Romaña
SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models. 287 - Marcela Uliano-Silva
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. 288 - Junwei Luo, Yading Feng, Xuyang Wu, Ruimin Li, Jiawei Shi, Wenjing Chang, Junfeng Wang:
ForestSubtype: a cancer subtype identifying approach based on high-dimensional genomic data and a parallel random forest. 289 - Nikitha Karkera, Sathwik Acharya, Sucheendra K. Palaniappan:
Leveraging pre-trained language models for mining microbiome-disease relationships. 290 - Irene Ortega-Sanz
CamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter. 291 - Adam J. H. Newton, David Chartash, Steven H. Kleinstein, Robert A. McDougal:
A pipeline for the retrieval and extraction of domain-specific information with application to COVID-19 immune signatures. 292 - Yue Wu, Xinran Ni, Zhihao Wang, Weike Feng:
Enhancing drug property prediction with dual-channel transfer learning based on molecular fragment. 293 - Senay Kafkas, Marwa Abdelhakim, Mahmut Uludag
Starvar: symptom-based tool for automatic ranking of variants using evidence from literature and genomes. 294 - Nuo Liu, Tonatiuh A. Gonzalez, Jacob Fischer, Chan Hong, Michelle Johnson
xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes. 295 - Xiu-e Gao, Jian-Gang Hu, Bo Chen, Yun-Ming Wang, Shengbin Zhou:
Causal discovery approach with reinforcement learning for risk factors of type II diabetes mellitus. 296 - Yan Li, Yinying Yao, Yu Xia, Mingjing Tang
Searching for protein variants with desired properties using deep generative models. 297 - Misung Yi, Tingting Zhan
Selection of optimal quantile protein biomarkers based on cell-level immunohistochemistry data. 298 - Christian D. Powell
The metabolomics workbench file status website: a metadata repository promoting FAIR principles of metabolomics data. 299 - Sven Berres, Jörg Gromoll, Marius Wöste, Sarah Sandmann
OGRE: calculate, visualize, and analyze overlap between genomic input regions and public annotations. 300 - Phasit Charoenkwan, Nalini Schaduangrat, Watshara Shoombuatong:
StackTTCA: a stacking ensemble learning-based framework for accurate and high-throughput identification of tumor T cell antigens. 301 - Yi Cheng, Xiuli Ma
Evaluating imputation methods for single-cell RNA-seq data. 302 - Alvin Farrel
ROGUE: an R Shiny app for RNA sequencing analysis and biomarker discovery. 303 - Ali H. Al-Fatlawi
Netrank: network-based approach for biomarker discovery. 304 - Fréderique Boeykens
VariantscanR: an R-package as a clinical tool for variant filtering of known phenotype-associated variants in domestic animals. 305 - Meghana V. Palukuri
Molecular complex detection in protein interaction networks through reinforcement learning. 306 - K. Syama
Correction: Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE. 307 - Huijing Yu, Zhenxian Zheng, Junhao Su, Tak Wah Lam
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP. 308 - Yabing Song, Jianbin Wang:
ggcoverage: an R package to visualize and annotate genome coverage for various NGS data. 309 - Jérémie Scire
estimateR: an R package to estimate and monitor the effective reproductive number. 310 - Michael J. Casey, Jörg Fliege
An information-theoretic approach to single cell sequencing analysis. 311 - Maria V. Meneses, Alberto Riva, Marco Salemi, Carla Mavian:
ARCA: the interactive database for arbovirus reported cases in the Americas. 312 - Suraiya Akhter
BaPreS: a software tool for predicting bacteriocins using an optimal set of features. 313 - Richard Border, Osman Asif Malik
rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating. 314 - Na Zhang, Juan Liu, Yu Jin, Wensi Duan, Ziling Wu, Zhaohui Cai, Meng Wu:
An adaptive multi-modal hybrid model for classifying thyroid nodules by combining ultrasound and infrared thermal images. 315 - Graham Alvare, Abiel Roche-Lima, Brian Fristensky
BioLegato: a programmable, object-oriented graphic user interface. 316 - Shelvasha Burkes-Patton, Elizabeth A. Cooper, Jessica Schlueter
RepBox: a toolbox for the identification of repetitive elements. 317 - Yunqing Liu
iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. 318 - Pinar Karadayi Atas:
A novel hybrid model to predict concomitant diseases for Hashimoto's thyroiditis. 319 - Joseph T. Vecchi
Sensitivity of CNN image analysis to multifaceted measurements of neurite growth. 320 - Sophie Le Bars
Predicting weighted unobserved nodes in a regulatory network using answer set programming. 321 - Haoyu Chen
Haplotype based testing for a better understanding of the selective architecture. 322 - Ying Qian, Xinyi Li, Jian Wu, Qian Zhang
MCL-DTI: using drug multimodal information and bi-directional cross-attention learning method for predicting drug-target interaction. 323 - Alexandre Renaux
A knowledge graph approach to predict and interpret disease-causing gene interactions. 324 - Jing Chen, Lianlian Wu, Kunhong Liu, Yong Xu, Song He, Xiaochen Bo:
EDST: a decision stump based ensemble algorithm for synergistic drug combination prediction. 325 - John K. L. Wong, Lena Jassowicz, Christel Herold-Mende, Martina Seiffert, Jan-Phillip Mallm, Peter Lichter, Marc Zapatka
scSNPdemux: a sensitive demultiplexing pipeline using single nucleotide polymorphisms for improved pooled single-cell RNA sequencing analysis. 326 - Tomás Bruna
Galba: genome annotation with miniprot and AUGUSTUS. 327 - Haitham Elmarakeby, Pavel S. Trukhanov, Vidal M. Arroyo
Empirical evaluation of language modeling to ascertain cancer outcomes from clinical text reports. 328 - Ali Ebrahimi
AUD-DSS: a decision support system for early detection of patients with alcohol use disorder. 329 - Tychele Turner:
Acorn: an R package for de novo variant analysis. 330 - Evgueni Jacob, Angélique Perrillat-Mercerot, Jean-Louis Palgen, Adèle L'Hostis, Nicoletta Ceres, Jean-Pierre Boissel, Jim Bosley, Cláudio Monteiro, Riad Kahoul:
Empirical methods for the validation of time-to-event mathematical models taking into account uncertainty and variability: application to EGFR + lung adenocarcinoma. 331 - Peng Du, Xiaofeng Niu, Xukun Li, Chiqing Ying, Yukun Zhou, Chang He, Shuangzhi Lv, Xiaoli Liu, Weibo Du
Automatically transferring supervised targets method for segmenting lung lesion regions with CT imaging. 332 - Yongxian Fan, Xiqian Lu, Guicong Sun:
IHCP: interpretable hepatitis C prediction system based on black-box machine learning models. 333 - Shourun Pan, Leiming Xia, Lei Xu, Zhen Li:
SubMDTA: drug target affinity prediction based on substructure extraction and multi-scale features. 334 - Shiyang Liang, Siwei Liu
HMCDA: a novel method based on the heterogeneous graph neural network and metapath for circRNA-disease associations prediction. 335 - Alvise Spanò
Rinmaker: a fast, versatile and reliable tool to determine residue interaction networks in proteins. 336 - Karlo Abnoosian
Prediction of diabetes disease using an ensemble of machine learning multi-classifier models. 337 - Binyou Wang, Jianmin Guo, Xiaofeng Liu, Yang Yu, Jianming Wu, Yiwei Wang:
Prediction of the effects of small molecules on the gut microbiome using machine learning method integrating with optimal molecular features. 338 - Xiaohong Wang, Xiaoli Jing
An approach for proteins and their encoding genes synonyms integration based on protein ontology. 339 - Nicholas J. Eagles, Richard Wilton, Andrew E. Jaffe, Leonardo Collado-Torres
BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data. 340 - Nirmal Singh Mahar, Rohit Satyam
A systematic comparison of human mitochondrial genome assembly tools. 341 - Juan Domingo
Scellpam: an R package/C++ library to perform parallel partitioning around medoids on scRNAseq data sets. 342 - Shuangshuang Xu
BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data. 343 - Layla Hosseini-Gerami
MAVEN: compound mechanism of action analysis and visualisation using transcriptomics and compound structure data in R/Shiny. 344 - Jidong Zhang, Bo Liu, Jiahui Wu, Zhihan Wang, Jianqiang Li:
DeepCAC: a deep learning approach on DNA transcription factors classification based on multi-head self-attention and concatenate convolutional neural network. 345 - Nouman Ahmad
Automatic segmentation of large-scale CT image datasets for detailed body composition analysis. 346 - Troy M. LaPolice
An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data. 347 - Han Bao, Jinhui Zhao, Xinjie Zhao, Chunxia Zhao
Prediction of plant secondary metabolic pathways using deep transfer learning. 348 - Nicholas K. O'Neill, Thor D. Stein, Junming Hu, Habbiburr Rehman, Joshua D. Campbell, Masanao Yajima, Xiaoling Zhang, Lindsay A. Farrer:
Bulk brain tissue cell-type deconvolution with bias correction for single-nuclei RNA sequencing data using DeTREM. 349 - Cheng Yong Tham, Touati Benoukraf
Correspondence on NanoVar's performance outlined by Jiang T. et al. in "Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation". 350 - Chen Zhou
ECL 3.0: a sensitive peptide identification tool for cross-linking mass spectrometry data analysis. 351 - Tao Jiang, Shiqi Liu, Hongzhe Guo:
Reply: Correspondence on NanoVar's performance outlined by Jiang T. et al. in 'Long-read sequencing settings for efficient structural variation detection based on comprehensive evaluation'. 352 - Jiahao Wang, Xiaodong Zhu, Kai Chen, Lei Hao, Yuanning Liu:
HAHNet: a convolutional neural network for HER2 status classification of breast cancer. 353 - Amira Al-Aamri
Critical assessment of on-premise approaches to scalable genome analysis. 354 - Kira J. Stanzick, Klaus J. Stark, Mathias Gorski, Johannes Schödel, René Krüger
KidneyGPS: a user-friendly web application to help prioritize kidney function genes and variants based on evidence from genome-wide association studies. 355 - Phasit Charoenkwan, Sasikarn Kongsompong, Nalini Schaduangrat, Pramote Chumnanpuen, Watshara Shoombuatong:
TIPred: a novel stacked ensemble approach for the accelerated discovery of tyrosinase inhibitory peptides. 356 - Jianan Sui, Jiazi Chen, Yuehui Chen, Naoki Iwamori, Jin Sun:
Identification of plant vacuole proteins by using graph neural network and contact maps. 357 - Anand K. Keshri, Rimanpreet Kaur, Suraj S. Rawat, Naina Arora, Rajan K. Pandey, Bajarang V. Kumbhar, Amit Mishra, Shweta Tripathi, Amit Prasad:
Designing and development of multi-epitope chimeric vaccine against Helicobacter pylori by exploring its entire immunogenic epitopes: an immunoinformatic approach. 358 - Völundur Hafstað, Jari Häkkinen
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data. 359 - Lina Ma, Sitao Zhang, Qi Liang
CrMP-Sol database: classification, bioinformatic analyses and comparison of cancer-related membrane proteins and their water-soluble variant designs. 360 - Shuwen Hu, Yi Jing, Tao Li, You-Gan Wang
Inferring circadian gene regulatory relationships from gene expression data with a hybrid framework. 362 - Lizhen Shao, Cong Fu, Xunying Chen:
A heterogeneous graph convolutional attention network method for classification of autism spectrum disorder. 363 - Sz-Wei Chu, Feng-Sheng Wang:
Fuzzy optimization for identifying antiviral targets for treating SARS-CoV-2 infection in the heart. 364 - Siti Nurmaini, Ade Iriani Sapitri, Bambang Tutuko, Muhammad Naufal Rachmatullah, Dian Palupi Rini, Annisa Darmawahyuni, Firdaus, Satria Mandala, Ria Nova, Nuswil Bernolian:
Automatic echocardiographic anomalies interpretation using a stacked residual-dense network model. 365 - Jiaxiang Jiang, Michael Goebel, Cezar Borba, William Smith, B. S. Manjunath:
A robust approach to 3D neuron shape representation for quantification and classification. 366 - Haixia Zhai, Hongli Hou, Junwei Luo, Xiaoyan Liu, Zhengjiang Wu, Junfeng Wang:
DGDTA: dynamic graph attention network for predicting drug-target binding affinity. 367 - Mathias Cardner
Predicting tumour content of liquid biopsies from cell-free DNA. 368 - Zhiwen Lu, Lu Guo, Jianhua Chen, Rongshu Wang:
Reference-based genome compression using the longest matched substrings with parallelization consideration. 369 - Eric Kofman, Brian Yee, Hugo C. Medina-Munoz, Gene W. Yeo
FLARE: a fast and flexible workflow for identifying RNA editing foci. 370 - Ignas Rumbavicius, Trine Rounge, Torbjørn Rognes:
HoCoRT: host contamination removal tool. 371 - Kiran Kumar Patro, Allam Jaya Prakash, Umamaheswararao Sanapala, Chaitanya Kumar Marpu, Nagwan M. Abdel Samee, Maali Alabdulhafith, Pawel Plawiak:
An effective correlation-based data modeling framework for automatic diabetes prediction using machine and deep learning techniques. 372 - F. Adriaan Lategan
SeqPredNN: a neural network that generates protein sequences that fold into specified tertiary structures. 373 - Zahra Ghorbanali
DrugRep-HeSiaGraph: when heterogenous siamese neural network meets knowledge graphs for drug repurposing. 374 - Junjun Zhang, Minzhu Xie:
Graph regularized non-negative matrix factorization with L2,1 norm regularization terms for drug-target interactions prediction. 375 - Monika Khandelwal, Ranjeet Kumar Rout:
PRMxAI: protein arginine methylation sites prediction based on amino acid spatial distribution using explainable artificial intelligence. 376 - Mikhail I. Schelkunov:
Mabs, a suite of tools for gene-informed genome assembly. 377 - Jianqiu Wu, Hongyang Chen, Minhao Cheng
CurvAGN: Curvature-based Adaptive Graph Neural Networks for Predicting Protein-Ligand Binding Affinity. 378 - Eman Ismail, Walaa K. Gad, Mohamed Hashem:
A hybrid Stacking-SMOTE model for optimizing the prediction of autistic genes. 379 - Molly G. Hayes, Morgan G. I. Langille, Hong Gu:
Cross-study analyses of microbial abundance using generalized common factor methods. 380 - Kipoong Kim, Tae-Hwan Jun, Bo-Keun Ha, Shuang Wang, Hokeun Sun:
New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits. 381 - A. Rohini, Carol Praveen, Sandeep Kumar Mathivanan, V. Muthukumaran, Saurav Mallik, Mohammed S. Alqahtani, Amal Al-Rasheed, Ben Othman Soufiene:
Multimodal hybrid convolutional neural network based brain tumor grade classification. 382 - Narumi Hatano, Mayumi Kamada, Ryosuke Kojima
Network-based prediction approach for cancer-specific driver missense mutations using a graph neural network. 383 - Ganghui Zhou, Jing Gao, Dongshi Zuo, Jin Li, Rui Li:
MSXFGP: combining improved sparrow search algorithm with XGBoost for enhanced genomic prediction. 384 - Chris C. R. Smith, Andrew D. Kern:
disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data. 385 - Luigi Di Biasi
Refactoring and performance analysis of the main CNN architectures: using false negative rate minimization to solve the clinical images melanoma detection problem. 386 - Xu Zhu, Lili Zhao, Lihong Huang, Wenxian Yang, Liansheng Wang, Rongshan Yu:
cgMSI: pathogen detection within species from nanopore metagenomic sequencing data. 387 - Vishakha Goyal
Unbiased image segmentation assessment toolkit for quantitative differentiation of state-of-the-art algorithms and pipelines. 388 - Pasquale Claudio Africa, Roberto Piersanti, Francesco Regazzoni
lifex-ep: a robust and efficient software for cardiac electrophysiology simulations. 389 - Dao-Feng Zhang, Wei He
EasyCGTree: a pipeline for prokaryotic phylogenomic analysis based on core gene sets. 390 - Élise Maigné, Céline Noirot, Julien Henry, Yaa Adu Kesewaah, Ludovic Badin, Sébastien Déjean
Asterics: a simple tool for the ExploRation and Integration of omiCS data. 391 - Rahi Jain, Wei Xu:
Artificial Intelligence based wrapper for high dimensional feature selection. 392 - Leonie Schürmeyer
Designs for the simultaneous inference of concentration-response curves. 393 - Yunqing Liu, Jiayi Zhao, Taylor Sterling Adams, Ningya Wang, Jonas Schupp, Weimiao Wu, John E. McDonough, Geoffrey Lowell Chupp, Naftali Kaminski, Zuoheng Wang, Xiting Yan
Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. 394 - Silvia Cascianelli, Gaia Ceddia, Alberto Marchesi, Marco Masseroli:
Identification of transcription factor high accumulation DNA zones. 395 - Valeriy Titarenko, Sofya Titarenko:
PerFSeeB: designing long high-weight single spaced seeds for full sensitivity alignment with a given number of mismatches. 396 - Jianhua Jia, Zhangying Wei, Mingwei Sun:
EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning. 397 - Charlie M. Carpenter, Lucas A. Gillenwater, Russell Bowler, Katerina J. Kechris, Debashis Ghosh:
TreeKernel: interpretable kernel machine tests for interactions between -omics and clinical predictors with applications to metabolomics and COPD phenotypes. 398 - Aurélie C. Lozano, Hantian Ding, Naoki Abe, Alexander E. Lipka:
Regularized multi-trait multi-locus linear mixed models for genome-wide association studies and genomic selection in crops. 399 - Lore Depuydt
Pan-genome de Bruijn graph using the bidirectional FM-index. 400 - Sadam Hussain
Deep learning, radiomics and radiogenomics applications in the digital breast tomosynthesis: a systematic review. 401 - Alexis Germán Murillo Carrasco
deltaXpress (ΔXpress): a tool for mapping differentially correlated genes using single-cell qPCR data. 402 - Óscar Castellanos-Rodríguez
SeQual-Stream: approaching stream processing to quality control of NGS datasets. 403 - William Kumler, Bryna J. Hazelton, Anitra E. Ingalls:
Picky with peakpicking: assessing chromatographic peak quality with simple metrics in metabolomics. 404 - Maryam Gholipour, Reza Khajouei, Parastoo Amiri, Sadrieh Hajesmaeel Gohari, Leila Ahmadian:
Extracting cancer concepts from clinical notes using natural language processing: a systematic review. 405 - Awwab Mohammad
Tri-model classifiers for EEG based mental task classification: hybrid optimization assisted framework. 406 - Hatice Yagmur Zengin, Erdem Karabulut:
Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance. 407 - Adrià Caballé-Mestres, Antoni Berenguer-Llergo
Roastgsa: a comparison of rotation-based scores for gene set enrichment analysis. 408 - Chenyu Ma, Yuanbo Shi, Yueyang Huang, Gongwei Dai:
Raman spectroscopy-based prediction of ofloxacin concentration in solution using a novel loss function and an improved GA-CNN model. 409 - Guohao Lv, Yingchun Xia, Zhao Qi, Zihao Zhao, Lianggui Tang, Cheng Chen, Shuai Yang, Qingyong Wang, Lichuan Gu:
LncRNA-protein interaction prediction with reweighted feature selection. 410 - Aritra Bose, Myson C. Burch, Agniva Chowdhury
Structure-informed clustering for population stratification in association studies. 411 - Robert J. Millikin
Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models. 412 - Joel Zirkle
Deep learning-enabled natural language processing to identify directional pharmacokinetic drug-drug interactions. 413 - Ximei Luo
Predicting active enhancers with DNA methylation and histone modification. 414 - Thomas A. Delomas, Stuart C. Willis:
Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data. 415 - Pietro Cinaglia
Multilayer network alignment based on topological assessment via embeddings. 416 - Hanjing Jiang, Yabing Huang, Qianpeng Li, Boyuan Feng:
ScLSTM: single-cell type detection by siamese recurrent network and hierarchical clustering. 417 - Irena Roterman, Katarzyna Stapor, Leszek Konieczny:
Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone. 418 - Pegah Mavaie, Lawrence Holder, Michael K. Skinner:
Hybrid deep learning approach to improve classification of low-volume high-dimensional data. 419 - Koki Tsuyuzaki, Manabu Ishii, Itoshi Nikaido:
Sctensor detects many-to-many cell-cell interactions from single cell RNA-sequencing data. 420 - Grégoire Prunier, Mehdi Cherkaoui, Albane Lysiak, Olivier Langella
Fast alignment of mass spectra in large proteomics datasets, capturing dissimilarities arising from multiple complex modifications of peptides. 421 - Thomas Binet, Séverine Padiolleau-Lefèvre
Comparative Study of Single-stranded Oligonucleotides Secondary Structure Prediction Tools. 422 - Yixin Zhang, Wei Liu, Weiliang Qiu:
A model-based clustering via mixture of hierarchical models with covariate adjustment for detecting differentially expressed genes from paired design. 423 - Noah Herrick, Susan Walsh:
ILIAD: a suite of automated Snakemake workflows for processing genomic data for downstream applications. 424 - Irena Roterman, Katarzyna Stapor, Leszek Konieczny:
Role of environmental specificity in CASP results. 425 - Yesol Sapozhnikov
Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability. 426 - Rongyuan Li, Jingli Wu, Gaoshi Li, Jiafei Liu, Junbo Xuan, Qi Zhu:
Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP. 427 - Xin Feng, Yihuai Cai
Optimizing diabetes classification with a machine learning-based framework. 428 - Linjun Chen, Xiao-Yuan Jing, Yaru Hao, Wei Liu, Xiaoke Zhu, Wei Han:
A novel two-way rebalancing strategy for identifying carbonylation sites. 429 - Ye Yuan, Qushuo Chen, Jun Mao, Guipeng Li
DG-Affinity: predicting antigen-antibody affinity with language models from sequences. 430 - Ruimin Wang
G-Aligner: a graph-based feature alignment method for untargeted LC-MS-based metabolomics. 431 - Gwangwoo Kim, Hyonho Chun:
Similarity-assisted variational autoencoder for nonlinear dimension reduction with application to single-cell RNA sequencing data. 432 - Orly Avraham, Tomer Tsaban, Ziv Ben-Aharon, Linoy Tsaban, Ora Schueler-Furman:
Protein language models can capture protein quaternary state. 433 - Zhichao Hou, Jiacheng Leng, Jiating Yu, Zheng Xia, Ling-Yun Wu:
PathExpSurv: pathway expansion for explainable survival analysis and disease gene discovery. 434 - Brijesh Kumar Sriwastava, Anup Kumar Halder
RUBic: rapid unsupervised biclustering. 435 - Luke Staniscia, Yun William Yu:
Image-centric compression of protein structures improves space savings. 437 - Jakob P. Pettersen
Genome-scale metabolic models reveal determinants of phenotypic differences in non-Saccharomyces yeasts. 438 - Ramin Amiri, Jafar Razmara
A novel efficient drug repurposing framework through drug-disease association data integration using convolutional neural networks. 442 - Elena Pianfetti, Marta Lovino, Elisa Ficarra, Loredana Martignetti:
MiREx: mRNA levels prediction from gene sequence and miRNA target knowledge. 443 - Mingwei Pang, Wangqiu He, Xufeng Lu, Yuting She, Liangxu Xie
CoDock-Ligand: combined template-based docking and CNN-based scoring in ligand binding prediction. 444 - Valentina Nale, Alice Chiodi
scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. 445 - Anup Kumar
Transformer-based tool recommendation system in Galaxy. 446 - 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. 447 - Danyi Chen, Xiaowen Wang, Hongming Zhu, Yizhi Jiang, Yulong Li, Qi Liu, Qin Liu:
Predicting anticancer synergistic drug combinations based on multi-task learning. 448 - Mahdi Pourmirzaei, Shahin Ramazi, Farzaneh Esmaili, Seyedehsamaneh Shojaeilangari
Machine learning-based approaches for ubiquitination site prediction in human proteins. 449 - 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. 450 - 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. 451 - 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. 452 - 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. 453 - Hui Sun, Yingfeng Zheng, Haonan Xie
PMFFRC: a large-scale genomic short reads compression optimizer via memory modeling and redundant clustering. 454 - 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. 455 - Hanhan Cong, Hong Liu, Yi Cao, Cheng Liang, Yuehui Chen:
Protein-protein interaction site prediction by model ensembling with hybrid feature and self-attention. 456 - Eduardo N. Castanho, João Lobo, Rui Henriques
G-bic: generating synthetic benchmarks for biclustering. 457 - 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. 458 - 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. 459 - Baptiste Turpin
Efficient design of synthetic gene circuits under cell-to-cell variability. 460 - Xuechun Xu
Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network. 461 - Yiyun Rao, Nabeel Ahmed, Justin Pritchard, Edward P. O'Brien:
Incorporating mutational heterogeneity to identify genes that are enriched for synonymous mutations in cancer. 462 - Kun Wang, Xiao Zhang, Hansen Cheng, Wenhao Ma, Guangchao Bao, Liting Dong, Yixiong Gou, Jian Yang
SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. 463 - Meng Zhang, Madhuri Sankaranarayanapillai, Jingcheng Du, Yang Xiang, Frank J. Manion, Marcelline R. Harris, Cooper Stansbury, Huy Anh Pham, Cui Tao
Machine learning-based donor permission extraction from informed consent documents. 477 - Diana Zarei
Subtyping irritable bowel syndrome using cluster analysis: a systematic review. 478 - Rajul Mahto, Saboor Uddin Ahmed, Rizwan ur Rahman, Rabia Musheer Aziz, Priyanka Roy
A novel and innovative cancer classification framework through a consecutive utilization of hybrid feature selection. 479 - Yining Liu, Yinuo Jin, Elham Azizi, Andrew J. Blumberg:
Cellstitch: 3D cellular anisotropic image segmentation via optimal transport. 480 - Zhen-Hao Guo
scInterpreter: a knowledge-regularized generative model for interpretably integrating scRNA-seq data. 481 - Michael J. Kane, Casey King, Denise Esserman, Nancy K. Latham, Erich J. Greene
A compressed large language model embedding dataset of ICD 10 CM descriptions. 482 - Chenqi Liao, Xiong Wang:
TCGAplot: an R package for integrative pan-cancer analysis and visualization of TCGA multi-omics data. 483 - Yingke Yang, Peiluan Li:
GPDRP: a multimodal framework for drug response prediction with graph transformer. 484 - Daniel Marrama, William D. Chronister, Luise Westernberg, Randi Vita, Zeynep Kosaloglu-Yalçin, Alessandro Sette, Morten Nielsen
PEPMatch: a tool to identify short peptide sequence matches in large sets of proteins. 485 - 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. 486 - Katerina Faltejsková
PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction. 487 - Warith Eddine Djeddi
Advancing drug-target interaction prediction: a comprehensive graph-based approach integrating knowledge graph embedding and ProtBert pretraining. 488 - Miaoshan Lu, Hengxuan Jiang, Ruimin Wang
Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation. 489 - 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. 490 - Daniel Dorey-Robinson, Giuseppe Maccari
IgMAT: immunoglobulin sequence multi-species annotation tool for any species including those with incomplete antibody annotation or unusual characteristics. 491 - Thummarat Paklao, Apichat Suratanee, Kitiporn Plaimas:
ICON-GEMs: integration of co-expression network in genome-scale metabolic models, shedding light through systems biology. 492 - Karolayne S. Azevedo, Luísa C. de Souza, Maria G. F. Coutinho, Raquel de M. Barbosa, Marcelo A. C. Fernandes:
Deepvirusclassifier: a deep learning tool for classifying SARS-CoV-2 based on viral subtypes within the coronaviridae family. 231 - Mike Blazanin
gcplyr: an R package for microbial growth curve data analysis. 232 - Robin Jugas
ProcaryaSV: structural variation detection pipeline for bacterial genomes using short-read sequencing. 233 - Louison Fresnais
A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques. 234 - Wend Yam Donald Davy Ouedraogo, Aïda Ouangraoua:
SimSpliceEvol2: alternative splicing-aware simulation of biological sequence evolution and transcript phylogenies. 235
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