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BMC Bioinformatics, Volume 23
Volume 23, Number 1, December 2022
- Brandon Reyes, Irene Otero-Muras, Vladislav A. Petyuk:
A numerical approach for detecting switch-like bistability in mass action chemical reaction networks with conservation laws. 1 - Shaoheng Liang, Jason Willis, Jinzhuang Dou, Vakul Mohanty, Yuefan Huang, Eduardo Vilar, Ken Chen
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Sensei: how many samples to tell a change in cell type abundance? 2 - Laurent S. V. Thomas
Correction to: Multi-template matching: a versatile tool for object-localization in microscopy images. 3 - Aparna Elangovan
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. 4 - Liugen Wang, Min Shang, Qi Dai, Pingan He
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks. 5 - M. A. Hakim Newton
Secondary structure specific simpler prediction models for protein backbone angles. 6 - Shiming Wang, Jie Li, Yadong Wang:
M2PP: a novel computational model for predicting drug-targeted pathogenic proteins. 7 - Zhaoying Chai, Han Jin, Shenghui Shi, Siyan Zhan, Lin Zhuo, Yu Yang:
Hierarchical shared transfer learning for biomedical named entity recognition. 8 - Han-Jing Jiang, Yabing Huang:
An effective drug-disease associations prediction model based on graphic representation learning over multi-biomolecular network. 9 - Gustavo Daniel Vega Magdaleno, Vladislav Bespalov, Yalin Zheng, Alex Alves Freitas, João Pedro de Magalhães:
Machine learning-based predictions of dietary restriction associations across ageing-related genes. 10 - Li Wang, Cheng Zhong:
gGATLDA: lncRNA-disease association prediction based on graph-level graph attention network. 11 - Nathan P. Gill, Raji Balasubramanian, James R. Bain
Path-level interpretation of Gaussian graphical models using the pair-path subscore. 12 - Johannes Hettich, J. Christof M. Gebhardt
Periodic synchronization of isolated network elements facilitates simulating and inferring gene regulatory networks including stochastic molecular kinetics. 13 - Yuliya Shapovalova, Tom Heskes, Tjeerd Dijkstra
Non-parametric synergy modeling of chemical compounds with Gaussian processes. 14 - Albert E. Zhou
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. 15 - Huijian Feng
scDIOR: single cell RNA-seq data IO software. 16 - Tulika Kakati
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning. 17 - Jörg Winkler
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. 18 - Junhui Qiu, Qi Zhou, Weicai Ye, Qianjun Chen
SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes. 19 - Jing Chen, Baotian Hu, Weihua Peng, Qingcai Chen
Biomedical relation extraction via knowledge-enhanced reading comprehension. 20 - Julia Vetter
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data. 21 - Vi Ngoc-Nha Tran
vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. 22 - Juan J. Lastra-Díaz
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. 23 - Yang Yu, Dezhou Kong:
Protein complexes detection based on node local properties and gene expression in PPI weighted networks. 24 - Atul Sharma, Pranjal Jain, Ashraf Mahgoub, Zihan Zhou, Kanak Mahadik, Somali Chaterji
Lerna: transformer architectures for configuring error correction tools for short- and long-read genome sequencing. 25 - Xuemin Dong, Shanshan Dong, Shengkai Pan, Xiangjiang Zhan:
RNA-combine: a toolkit for comprehensive analyses on transcriptome data from different sequencing platforms. 26 - Renmao Tian, Behzad Imanian
ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently. 27 - James J. Yang, Xi Luo, Elisa M. Trucco
Polygenic risk prediction based on singular value decomposition with applications to alcohol use disorder. 28 - Xifang Sun, Donglin Wang, Jiaqiang Zhu
A novel nonparametric computational strategy for identifying differential methylation regions. 29 - Xiong Yuan, Zirong Li, Liwen Xiong
Effective identification of varieties by nucleotide polymorphisms and its application for essentially derived variety identification in rice. 30 - Lu Li, Huub C. J. Hoefsloot, Albert A. de Graaf, Evrim Acar, Age K. Smilde
Exploring dynamic metabolomics data with multiway data analysis: a simulation study. 31 - Katrin Madjar
Correction to: Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. 32 - Lakshay Anand
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes. 33 - Fei Song, Shiyin Tan
Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks. 34 - Miaoshan Lu
Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time. 35 - Lucille Lopez-Delisle
baredSC: Bayesian approach to retrieve expression distribution of single-cell data. 36 - Jeremy J. Yang, Christopher Gessner, Joel Duerksen, Daniel Biber, Jessica L. Binder, Murat Ozturk, Brian Foote, Robin McEntire, Kyle Stirling, Ying Ding, David J. Wild:
Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. 37 - Emily Kaczmarek, Jina Nanayakkara, Alireza Sedghi, Mehran Pesteie, Thomas Tuschl, Neil Renwick
Topology preserving stratification of tissue neoplasticity using Deep Neural Maps and microRNA signatures. 38 - Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany, Sol Schvartzman
MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. 39 - Ludwig Mann
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. 40 - Maia H. Malonzo
LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis. 41 - Mehrdad Mansouri, Sahand Khakabimamaghani, Leonid Chindelevitch
Aristotle: stratified causal discovery for omics data. 42 - Elena Rojano, Fernando Moreno Jabato
Assigning protein function from domain-function associations using DomFun. 43 - Vy Nguyen
scAnnotatR: framework to accurately classify cell types in single-cell RNA-sequencing data. 44 - Xiaopu Zhang, Musa A. Hassan, James G. D. Prendergast
Using machine learning to detect the differential usage of novel gene isoforms. 45 - Michael Y. Lee, Jacob S. Bedia
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images. 46 - Il-Hyung Lee
Intelligent fluorescence image analysis of giant unilamellar vesicles using convolutional neural network. 48 - Brandon Signal
how_are_we_stranded_here: quick determination of RNA-Seq strandedness. 49 - Albert Rosenberger
Iam hiQ - a novel pair of accuracy indices for imputed genotypes. 50 - Zhaonan Zou
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. 51 - Gavin Mackenzie, Rasmus W. Jensen
Varia: a tool for prediction, analysis and visualisation of variable genes. 52 - Niloofar Borhani, Jafar Ghaisari, Maryam Abedi, Marzieh Kamali, Yousof Gheisari
A deep learning approach to predict inter-omics interactions in multi-layer networks. 53 - Himangi Srivastava
NetSeekR: a network analysis pipeline for RNA-Seq time series data. 54 - Sonja Mathias
CBMOS: a GPU-enabled Python framework for the numerical study of center-based models. 55 - Xianwei Pan, Peng Huang, Shan Li, Lei Cui:
MCRWR: a new method to measure the similarity of documents based on semantic network. 56 - Andrew Walakira
Detecting gene-gene interactions from GWAS using diffusion kernel principal components. 57 - Mehdi Saman Booy, Alexander Ilin, Pekka Orponen
RNA secondary structure prediction with convolutional neural networks. 58 - Sanna Abrahamsson
PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data. 59 - Cinzia Klemm, Rowan S. M. Howell
ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens. 60 - Luis Kuhn Cuellar
A data management infrastructure for the integration of imaging and omics data in life sciences. 61 - Walker Gussler, David S. Campo
Primary case inference in viral outbreaks through analysis of intra-host variant population. 62 - Liyu Liu, Meng Si, Hecheng Ma, Menglin Cong, Quanzheng Xu, Qinghua Sun, Weiming Wu, Cong Wang, Michael J. Fagan, Luis A. J. Mur, Qing Yang, Bing Ji
A hierarchical opportunistic screening model for osteoporosis using machine learning applied to clinical data and CT images. 63 - Jia-Ming Chang
HiCmapTools: a tool to access HiC contact maps. 64 - Juliane Pfeil, Alina S. Nechyporenko
Examination of blood samples using deep learning and mobile microscopy. 65 - Yuan Jin, Yang Yang:
ProtPlat: an efficient pre-training platform for protein classification based on FastText. 66 - Alejandro Thérèse Navarro
Multiallelic models for QTL mapping in diverse polyploid populations. 67 - Min Xie
gcaPDA: a haplotype-resolved diploid assembler. 68 - Ziyin Xin, Yujun Cai, Louis T. Dang
MonaGO: a novel gene ontology enrichment analysis visualisation system. 69 - Cheng Peng, Xinben Zhang, Zhijian Xu, Zhaoqiang Chen, Yanqing Yang
D3PM: a comprehensive database for protein motions ranging from residue to domain. 70 - Basak Kocaoglu, William H. Alexander:
Degeneracy measures in biologically plausible random Boolean networks. 71 - Xiaoquan Chu
Prediction of liquid-liquid phase separating proteins using machine learning. 72 - Umberto Ferraro Petrillo, Francesco Palini, Giuseppe Cattaneo, Raffaele Giancarlo:
Correction to: FASTA/Q data compressors for MapReduce-Hadoop genomics: space and time savings made easy. 73 - Hans Müller Paul, Dave D. Istanto, Jacob R Heldenbrand, Matthew E. Hudson
CROPSR: an automated platform for complex genome-wide CRISPR gRNA design and validation. 74 - Zun Liu, Xing-Nan Wang, Hui Yu
Predict multi-type drug-drug interactions in cold start scenario. 75 - Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. 76 - Olivér M. Balogh
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model. 78 - Jakob P. Pettersen
csdR, an R package for differential co-expression analysis. 79 - Leonardo R. Souza
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins. 80 - Modupeore O. Adetunji
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. 77 - Jie Hou
Distance correlation application to gene co-expression network analysis. 81 - Raphaël Mourad:
TADreg: a versatile regression framework for TAD identification, differential analysis and rearranged 3D genome prediction. 82 - Omer Ali, Amna Farooq, Mingyi Yang
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. 83 - Florin Ratajczak
Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. 84 - Wiktor Kusmirek
CNVind: an open source cloud-based pipeline for rare CNVs detection in whole exome sequencing data based on the depth of coverage. 85 - Quang-Huy Nguyen
DrGA: cancer driver gene analysis in a simpler manner. 86 - Hui Zhang, Shan Gao, Weiyang Chen:
Automated recognition and analysis of head thrashes behavior in C. elegans. 87 - Chengcheng Zhang, Yao Lu, Tianyi Zang
CNN-DDI: a learning-based method for predicting drug-drug interactions using convolution neural networks. 88 - Ningyi Zhang, Tianyi Zang
A multi-network integration approach for measuring disease similarity based on ncRNA regulation and heterogeneous information. 89 - Mohammad Neamul Kabir
EnsembleFam: towards more accurate protein family prediction in the twilight zone. 90 - Shang Liu
Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development. 91 - Adil Al-Azzawi
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. 92 - Yiyu Hong, Juyong Lee
A-Prot: protein structure modeling using MSA transformer. 93 - Francis C. Motta, Robert C. Moseley, Bree Cummins, Anastasia Deckard
Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. 94 - Robert Logan
3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data. 95 - Michela Quadrini, Sebastian Daberdaku
Hierarchical representation for PPI sites prediction. 96 - Michael Lau
Evaluation of tree-based statistical learning methods for constructing genetic risk scores. 97 - Malcolm E. Fisher
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. 99 - Katarzyna Stapor
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. 100 - Lindsay V. Clark, Wittney Mays, Alexander E. Lipka
A population-level statistic for assessing Mendelian behavior of genotyping-by-sequencing data from highly duplicated genomes. 101 - Xinyue Qi, Shouhao Zhou, Martyn Plummer:
On Bayesian modeling of censored data in JAGS. 102 - Wuming Gong
Single cell lineage reconstruction using distance-based algorithms and the R package, DCLEAR. 103 - Yun Chao Lin, Ansaf Salleb-Aouissi, Thomas Hooven:
Interpretable prediction of necrotizing enterocolitis from machine learning analysis of premature infant stool microbiota. 104 - Mathisca C. M. de Gunst, Michel Mandjes, Birgit Sollie:
Statistical inference for a quasi birth-death model of RNA transcription. 105 - Elliott Swanson
BarWare: efficient software tools for barcoded single-cell genomics. 106 - David Chisanga, Yang Liao, Wei Shi:
Impact of gene annotation choice on the quantification of RNA-seq data. 107 - Jimmy Ka Ho Chiu, Rick Twee-Hee Ong:
Clustering biological sequences with dynamic sequence similarity threshold. 108 - Honglan Li, Seungjin Na, Kyu-Baek Hwang
TIDD: tool-independent and data-dependent machine learning for peptide identification. 109 - Josip Rudar
LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. 110 - Stefano Marchesin
TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction. 111 - Xu Yang, Masahiro Kasahara
LPMX: a pure rootless composable container system. 112 - Ana B. Romero-Losada, Christina Arvanitidou
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. 113 - Gerard P. Quinn, Tamas Sessler, Baharak Ahmaderaghi, Shauna Lambe, Harper VanSteenhouse, Mark Lawler
classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes. 114 - Bolin Wang, Yuanyuan Sun, Yonghe Chu, Di Zhao, Zhihao Yang, Jian Wang:
Refining electronic medical records representation in manifold subspace. 115 - Mikhail D. Magnitov
Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments. 116 - Borja González-Seoane
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models. 117 - Raul I. Perez Martell, Alison Ziesel, Hosna Jabbari
Supervised promoter recognition: a benchmark framework. 118 - Viivi Halla-aho, Harri Lähdesmäki:
Probabilistic modeling methods for cell-free DNA methylation based cancer classification. 119 - Peng Su, K. Vijay-Shanker:
Investigation of improving the pre-training and fine-tuning of BERT model for biomedical relation extraction. 120 - E. Amiri Souri, Roman Laddach, S. N. Karagiannis
Novel drug-target interactions via link prediction and network embedding. 121 - Don Neumann, Anireddy S. N. Reddy
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. 142 - Forough Firoozbakht, Iman Rezaeian, Luis Rueda
Computationally repurposing drugs for breast cancer subtypes using a network-based approach. 143 - Usman Naseem
Benchmarking for biomedical natural language processing tasks with a domain specific ALBERT. 144 - James W. Webber, Kevin M. Elias:
Fast and robust imputation for miRNA expression data using constrained least squares. 145 - Ying Ji, Rui Chen, Quan Wang, Qiang Wei, Ran Tao, Bingshan Li:
A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization. 146 - Micha Hersch, Adriano Biasini
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. 147 - Alessia Auriemma Citarella
SNARER: new molecular descriptors for SNARE proteins classification. 148 - Kyle Fletcher, Rongkui Han, Diederik Smilde, Richard Michelmore:
Variance of allele balance calculated from low coverage sequencing data infers departure from a diploid state. 150 - Fabrizio Frasca, Matteo Matteucci, Michele Leone
Accurate and highly interpretable prediction of gene expression from histone modifications. 151 - Meiling Liu, Juna Goo, Yang Liu, Wei Sun, Michael C. Wu
TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes. 152 - Jin-Ok Lee
tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data. 155 - John A. Hadish, Tyler Biggs, Benjamin T. Shealy, M. Reed Bender, Coleman McKnight, Connor Wytko, Melissa C. Smith, F. Alex Feltus, Loren A. Honaas
GEMmaker: process massive RNA-seq datasets on heterogeneous computational infrastructure. 156 - Jaeyong Choi, Woochan Lee, Jung-Ki Yoon, Sun Mi Choi, Chang-Hoon Lee, Hyeong-Gon Moon
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data. 157 - Mateo Gray
KnotAli: informed energy minimization through the use of evolutionary information. 159 - Lei Deng, Zixuan Liu, Yurong Qian, Jingpu Zhang:
Predicting circRNA-drug sensitivity associations via graph attention auto-encoder. 160 - Jiayi Dong, Yin Zhang, Fei Wang:
scSemiAE: a deep model with semi-supervised learning for single-cell transcriptomics. 161 - Xiaodan Zhang, Jinxiang Xuan, Chensong Yao, Qijuan Gao, Lianglong Wang, Xiu Jin, Shaowen Li:
A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model. 162 - Yongsun Shim, Munhwan Lee, Pil-Jong Kim, Hong-Gee Kim
A novel approach to predicting the synergy of anti-cancer drug combinations using document-based feature extraction. 163 - Tai-Wei Chiang, Te-Lun Mai
CircMiMi: a stand-alone software for constructing circular RNA-microRNA-mRNA interactions across species. 164 - Xiaohan Jiang, Xiujun Zhang
RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. 165 - Paola Paci
SPINNAKER: an R-based tool to highlight key RNA interactions in complex biological networks. 166 - Riku Walve, Leena Salmela
HGGA: hierarchical guided genome assembler. 167 - Haileab Hilafu, Sandra E. Safo
Sparse sliced inverse regression for high dimensional data analysis. 168 - Eric B. Fauman, Craig Hyde:
An optimal variant to gene distance window derived from an empirical definition of cis and trans protein QTLs. 169 - Junyao Kuang, Nicolas Buchon, Kristin Michel
A global $Anopheles\ gambiae$ gene co-expression network constructed from hundreds of experimental conditions with missing values. 170 - Gustavo Sganzerla Martinez
Machine learning and statistics shape a novel path in archaeal promoter annotation. 171 - Nikola Benes
Exploring attractor bifurcations in Boolean networks. 173 - Niina Smolander, Timothy R. Julian, Manu V. Tamminen
Prider: multiplexed primer design using linearly scaling approximation of set coverage. 174 - Suli Liu, Wu Yao
Prediction of lung cancer using gene expression and deep learning with KL divergence gene selection. 175 - Xiao Chu, Mao Jiang, Zhuo-Jun Liu:
Biomarker interaction selection and disease detection based on multivariate gain ratio. 176 - Mindan Xing, Jia Li:
Diagnostic and prognostic values of pyroptosis-related genes for the hepatocellular carcinoma. 177 - Huilong Chen, Xiaoming Song, Qian Shang, Shuyan Feng, Weina Ge:
CFVisual: an interactive desktop platform for drawing gene structure and protein architecture. 178 - Jonathan P. Dekermanjian, Elin Shaddox, Debmalya Nandy, Debashis Ghosh, Katerina J. Kechris:
Mechanism-aware imputation: a two-step approach in handling missing values in metabolomics. 179 - Reji Manjunathan, Vijayalakshmi Periyaswami, Kartik Mitra
Molecular docking analysis reveals the functional inhibitory effect of Genistein and Quercetin on TMPRSS2: SARS-COV-2 cell entry facilitator spike protein. 180 - Hao Qian, Nanxue Cui, Qiao Zhou, Shihai Zhang:
Identification of miRNA biomarkers for stomach adenocarcinoma. 181 - Juan Carlos Aledo
renz: An R package for the analysis of enzyme kinetic data. 182 - Yunchuan Wang
PGD: a machine learning-based photosynthetic-related gene detection approach. 183 - Eliot Y. Zhu, Adam J. Dupuy
Machine learning approach informs biology of cancer drug response. 184 - Lekang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang:
DeSP: a systematic DNA storage error simulation pipeline. 185 - Ruixue Hou, Lewis E. Tomalin
Correction: cosinoRmixedeffects: an R package for mixed-effects cosinor models. 186 - Juhyeon Kim, Saeyeon Cheon, Insung Ahn:
NGS data vectorization, clustering, and finding key codons in SARS-CoV-2 variations. 187 - Petr Smirnov, Ian Smith
Evaluation of statistical approaches for association testing in noisy drug screening data. 188 - Ying Liang
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model. 189 - Federica Conte, Federico Papa
StaRTrEK: in silico estimation of RNA half-lives from genome-wide time-course experiments without transcriptional inhibition. 190 - Julius B. Kirkegaard
Simultant: simultaneous curve fitting of functions and differential equations using analytical gradient calculations. 191 - Eduardo N. Castanho
Biclustering fMRI time series: a comparative study. 192 - Wen-Yi Yu, Yu Zhang, Meng-Kai Li, Zi-Ying Yang, Wing Kam Fung, Pei-Zhen Zhao, Ji-Yuan Zhou
BEXCIS: Bayesian methods for estimating the degree of the skewness of X chromosome inactivation. 193 - Yi-Hua Jiang, Jie Long, Zhi-bin Zhao, Liang Li
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis. 194 - Michael Skuhersky, Tailin Wu, Eviatar Yemini, Amin Nejatbakhsh, Edward S. Boyden, Max Tegmark:
Toward a more accurate 3D atlas of C. elegans neurons. 195 - Ilya Plyusnin
ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. 196 - Jayadev Joshi
PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling. 197 - Felix Van der Jeugt
FragGeneScanRs: faster gene prediction for short reads. 198 - Sai Hu, Zhihong Zhang, Hui-jun Xiong, Meiping Jiang, Yingchun Luo, Wei Yan, Bihai Zhao:
A tensor-based bi-random walks model for protein function prediction. 199 - Alfonso Rojas Domínguez
Modeling cancer immunoediting in tumor microenvironment with system characterization through the ising-model Hamiltonian. 200 - Chao Li, Jinxing Li, Jun Sun, Li Mao, Vasile Palade, Bilal Ahmad:
Parallel multi-swarm cooperative particle swarm optimization for protein-ligand docking and virtual screening. 201 - Jie-Huei Wang
Overlapping group screening for detection of gene-environment interactions with application to TCGA high-dimensional survival genomic data. 202 - Mariusz Marzec, Adam Piórkowski, Arkadiusz Gertych
Efficient automatic 3D segmentation of cell nuclei for high-content screening. 203 - Laura Puente-Santamaria
Hypoxia classifier for transcriptome datasets. 204 - Edwin S. Dalmaijer
Statistical power for cluster analysis. 205 - Pablo Flores
An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment. 207 - Zachary R. McCaw
Fitting Gaussian mixture models on incomplete data. 208 - Andrea Hita, Gilles Brocart, Ana Fernandez, Marc Rehmsmeier, Anna Alemany, Sol Schvartzman
Correction: MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts. 209 - Shaina Raza, Brian Schwartz, Laura C. Rosella:
CoQUAD: a COVID-19 question answering dataset system, facilitating research, benchmarking, and practice. 210 - Kurt J. P. Espinosa, Panagiotis Georgiadis
Comparing neural models for nested and overlapping biomedical event detection. 211 - Ran Liu, Miye Wang, Tao Zheng, Rui Zhang, Nan Li, Zhongxiu Chen, Hongmei Yan, Qingke Shi:
An artificial intelligence-based risk prediction model of myocardial infarction. 217 - Seo Hyun Shin, Seung Man Oh, Jung Han Yoon Park, Ki Won Lee, Hee Yang:
OptNCMiner: a deep learning approach for the discovery of natural compounds modulating disease-specific multi-targets. 218 - Yi Niu, Mingming Ma, Fu Li, Xianming Liu, Guangming Shi:
ACO: lossless quality score compression based on adaptive coding order. 219 - Magnus D. Vigeland:
QuickPed: an online tool for drawing pedigrees and analysing relatedness. 220 - Honglei Wang, Hui Liu, Tao Huang, Gangshen Li, Lin Zhang, Yanjing Sun:
EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction. 221 - Yu Wang, Zhengxiao Wei, Lei Xi:
Sfcnn: a novel scoring function based on 3D convolutional neural network for accurate and stable protein-ligand affinity prediction. 222 - Quynh T. Tran, Md. Zahangir Alom, Brent A. Orr:
Comprehensive study of semi-supervised learning for DNA methylation-based supervised classification of central nervous system tumors. 223 - Changxiang He, Yuru Liu, Hao Li, Hui Zhang, Yaping Mao
Multi-type feature fusion based on graph neural network for drug-drug interaction prediction. 224 - Matthis Ebel
Global, highly specific and fast filtering of alignment seeds. 225 - Kulwadee Thanamit, Franziska Hörhold, Marcus Oswald, Rainer König:
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. 226 - Felix Kallenborn
CARE 2.0: reducing false-positive sequencing error corrections using machine learning. 227 - Verena E. Kutschera
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. 228 - Steven Gore
CancerNet: a unified deep learning network for pan-cancer diagnostics. 229 - Yu Zhang, Xiao Chang, Jie Xia, Yanhong Huang, Shaoyan Sun, Luonan Chen, Xiaoping Liu
Identifying network biomarkers of cancer by sample-specific differential network. 230 - Rebeca Queiroz Figueiredo, Sara Díaz del Ser, Tamara Raschka, Martin Hofmann-Apitius, Alpha Tom Kodamullil, Sarah Mubeen, Daniel Domingo-Fernández
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. 231 - Yingnan Han
Empowering the discovery of novel target-disease associations via machine learning approaches in the open targets platform. 232 - Alfred Ultsch, Jörn Lötsch
Euclidean distance-optimized data transformation for cluster analysis in biomedical data (EDOtrans). 233 - Xiao-Rui Su, Lun Hu, Zhu-Hong You, Pengwei Hu, Bo-Wei Zhao:
Multi-view heterogeneous molecular network representation learning for protein-protein interaction prediction. 234 - Sarah Samorodnitsky, Katherine A. Hoadley, Eric F. Lock:
A hierarchical spike-and-slab model for pan-cancer survival using pan-omic data. 235 - Ayoub Lasri
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation. 236 - Nelson R. C. Monteiro
Explainable deep drug-target representations for binding affinity prediction. 237 - Xinyue Qi, Shouhao Zhou, Martyn Plummer:
Correction: On Bayesian modeling of censored data in JAGS. 238 - Sofia Persson
rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. 239 - H. Busra Cagirici, Hikmet Budak
G4Boost: a machine learning-based tool for quadruplex identification and stability prediction. 240 - Yusuf Khan, Daniel Hammarström, Stian Ellefsen, Rafi Ahmad
Normalization of gene expression data revisited: the three viewpoints of the transcriptome in human skeletal muscle undergoing load-induced hypertrophy and why they matter. 241 - Wei Dai, Cai Li, Ting Li, Jianchang Hu, Heping Zhang
Super-taxon in human microbiome are identified to be associated with colorectal cancer. 243 - Guanghui Li, Tao Fang, Yuejin Zhang, Cheng Liang, Qiu Xiao, Jiawei Luo:
Predicting miRNA-disease associations based on graph attention network with multi-source information. 244 - Jehad Aldahdooh
Using BERT to identify drug-target interactions from whole PubMed. 245 - Vladimir Nikolic, Amirhossein Afshinfard, Justin Chu, Johnathan Wong
RResolver: efficient short-read repeat resolution within ABySS. 246 - Binglin Cheng, Peitao Zhou, Yuhan Chen:
Machine-learning algorithms based on personalized pathways for a novel predictive model for the diagnosis of hepatocellular carcinoma. 248 - Delong Zhou, Yvan Tran, Sherif Abou Elela, Michelle S. Scott:
SAPFIR: A webserver for the identification of alternative protein features. 250 - Zeeshan Shaukat
A state-of-the-art technique to perform cloud-based semantic segmentation using deep learning 3D U-Net architecture. 251 - Gang Chi, Jin-Hong Pei, Xue-Qing Li:
RAE1 is a prognostic biomarker and is correlated with clinicopathological characteristics of patients with hepatocellular carcinoma. 252 - Shaked Naor-Hoffmann, Dina Svetlitsky, Neta Sal-Man, Yaron Orenstein, Michal Ziv-Ukelson:
Predicting the pathogenicity of bacterial genomes using widely spread protein families. 253 - Anthony F. Herzig
Moment estimators of relatedness from low-depth whole-genome sequencing data. 254 - Zachary R. McCaw, Hugues Aschard, Hanna Julienne
Correction: Fitting Gaussian mixture models on incomplete data. 255 - Shengrong Xia, Yingchun Xia, Chulei Xiang, Hui Wang, Chao Wang, Jin He, Guolong Shi, Lichuan Gu
A virus-target host proteins recognition method based on integrated complexes data and seed extension. 256 - Jidong Zhang, Bo Liu, Zhihan Wang, Klaus Lehnert, Mark Gahegan:
DeepPN: a deep parallel neural network based on convolutional neural network and graph convolutional network for predicting RNA-protein binding sites. 257 - Ying Liang
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction. 258 - Jinghang Gu
Multi-probe attention neural network for COVID-19 semantic indexing. 259 - Chao Jin, Hao Zhang, Ling Yin, Yong Zhang, Shengzhong Feng:
Optimize data-driven multi-agent simulation for COVID-19 transmission. 260 - Emiliano A. Videla Rodriguez, Fábio Pértille
Practical application of a Bayesian network approach to poultry epigenetics and stress. 261 - Blaise Hanczar, Victoria Bourgeais
Assessment of deep learning and transfer learning for cancer prediction based on gene expression data. 262 - Isabel Segura-Bedmar, David Camino-Perdonas, Sara Guerrero-Aspizua:
Exploring deep learning methods for recognizing rare diseases and their clinical manifestations from texts. 263 - Mohammad H. Alshayeji
CAD systems for COVID-19 diagnosis and disease stage classification by segmentation of infected regions from CT images. 264 - Soichiro Nishiyama, Kengo Sato, Ryutaro Tao:
Integer programming for selecting set of informative markers in paternity inference. 265 - Yue Jiang, Yuxuan Wang, Lin Shen, Donald A. Adjeroh, Zhidong Liu, Jie Lin:
Identification of all-against-all protein-protein interactions based on deep hash learning. 266 - Konstantinos Tzanakis
MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data. 267 - Vincent Moco, Damien Cazenave, Maëlle Garnier, Matthieu Pot, Isabel Marcelino
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories. 268 - Fabrizio Angaroni
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. 269 - Jingyang Niu, Jing Yang, Yuyu Guo, Kun Qian, Qian Wang:
Joint deep learning for batch effect removal and classification toward MALDI MS based metabolomics. 270 - Haisong Feng, Ying Xiang, Xiaosong Wang, Wei Xue, Zhenyu Yue
MTAGCN: predicting miRNA-target associations in Camellia sinensis var. assamica through graph convolution neural network. 271 - Yongxian Fan, Binchao Peng:
StackEPI: identification of cell line-specific enhancer-promoter interactions based on stacking ensemble learning. 272 - Noureldin S. Eissa, Uswah Khairuddin, Rubiyah Yusof:
A hybrid metaheuristic-deep learning technique for the pan-classification of cancer based on DNA methylation. 273 - Lekang Yuan, Zhen Xie, Ye Wang
Correction to: DeSP: a systematic DNA storage error simulation pipeline. 274 - Junaid Rashid
A novel multiple kernel fuzzy topic modeling technique for biomedical data. 275 - Ronghui Li, Bella Banjanin, Rebekka K. Schneider
Detection of cell markers from single cell RNA-seq with sc2marker. 276 - Chenye Wang
DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph. 277 - Reza Hassanzadeh
Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency? 278 - Maximilian Sprang
Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. 279 - Kai Du, Pindong Chen, Kun Zhao, Yida Qu, Xiaopeng Kang, Yong Liu
Impaired time-distance reconfiguration patterns in Alzheimer's disease: a dynamic functional connectivity study with 809 individuals from 7 sites. 280 - Muhammad Tuan Amith, Licong Cui, Degui Zhi, Kirk Roberts, Xiaoqian Jiang, Fang Li, Evan Yu, Cui Tao
Toward a standard formal semantic representation of the model card report. 281 - Hua Chen, Juan Liu, Chunbing Hua, Jing Feng, Baochuan Pang, Dehua Cao, Cheng Li:
Accurate classification of white blood cells by coupling pre-trained ResNet and DenseNet with SCAM mechanism. 282 - Sajid Mahmud, Zhiye Guo, Farhan Quadir
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps. 283 - Huiping Shi, Liang Gao
Identification and validation of a siglec-based and aging-related 9-gene signature for predicting prognosis in acute myeloid leukemia patients. 284 - Brendan O'Fallon
Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data. 285 - Daniel Flatschacher
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data. 286 - Konstantin Bob
Locality-sensitive hashing enables efficient and scalable signal classification in high-throughput mass spectrometry raw data. 287 - Hamas A. AL-kuhali, Ma Shan, Mohanned Abduljabbar Hael
Multiview clustering of multi-omics data integration by using a penalty model. 288 - Tuomas Kaseva
Marker-controlled watershed with deep edge emphasis and optimized H-minima transform for automatic segmentation of densely cultivated 3D cell nuclei. 289 - Stephen Coleman, Paul D. W. Kirk, Chris Wallace:
Consensus clustering for Bayesian mixture models. 290 - Marcin Malec, Hasan Kurban
ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data. 291 - Stefan Röder
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses. 292 - Ozan Ozisik
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. 293 - Hansen Chen, Jianhua Chen
CMIC: an efficient quality score compressor with random access functionality. 294 - Alessio Mascolini, Dario Cardamone
Exploiting generative self-supervised learning for the assessment of biological images with lack of annotations. 295 - Chamila Perera, Haixiang Zhang, Yinan Zheng, Lifang Hou, Annie Qu, Cheng Zheng, Ke Xie
HIMA2: high-dimensional mediation analysis and its application in epigenome-wide DNA methylation data. 296 - Haichang Yao, GuangYong Hu, Shangdong Liu, Houzhi Fang, Yimu Ji:
SparkGC: Spark based genome compression for large collections of genomes. 297 - Amin Ghareyazi
Pan-cancer integrative analysis of whole-genome De novo somatic point mutations reveals 17 cancer types. 298 - Dan Huang, Ji-Yong An, Lei Zhang, Bailong Liu:
Computational method using heterogeneous graph convolutional network model combined with reinforcement layer for MiRNA-disease association prediction. 299 - Xiaoxu Wang, Yijia Zhang, Peixuan Zhou, Xiaoxia Liu:
A supervised protein complex prediction method with network representation learning and gene ontology knowledge. 300 - M. Walder, E. Edelstein, M. Carroll
Integrated structure-based protein interface prediction. 301 - Katherine James
Integration of probabilistic functional networks without an external Gold Standard. 302 - Weidong Xie
A novel biomarker selection method combining graph neural network and gene relationships applied to microarray data. 303 - Adam N. Bennett
Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files. 304 - Ronald de Vlaming
Multivariate estimation of factor structures of complex traits using SNP-based genomic relationships. 305 - Jian Wen, Lijia Wan, Xieping Dong
The prognostic value of autophagy related genes with potential protective function in Ewing sarcoma. 306 - Tobias Hepp
Mixture density networks for the indirect estimation of reference intervals. 307 - Xinyu He
A biomedical event extraction method based on fine-grained and attention mechanism. 308 - Li Lin, Liye Zhang:
Joint analysis of scATAC-seq datasets using epiConv. 309 - Anna Hutchinson, James Liley, Chris Wallace
fcfdr: an R package to leverage continuous and binary functional genomic data in GWAS. 310 - Samira Sanami
In silico design of a multi-epitope vaccine against HPV16/18. 311 - Jiacheng Wu, Ni Li, Linwen Zhu, Dawei Zhen, Mengqi Li, Hang Chen
Multiple roles of apolipoprotein B mRNA editing enzyme catalytic subunit 3B (APOBEC3B) in human tumors: a pan-cancer analysis. 312 - Merlin Bardin, Pierre Rousselot-Pailley, Thierry Tron, Viviane Robert:
Investigation of dirigent like domains from bacterial genomes. 313 - Yuni Zeng, Xiangru Chen, Dezhong Peng, Lijun Zhang, Haixiao Huang:
Multi-scaled self-attention for drug-target interaction prediction based on multi-granularity representation. 314 - Annika Bürger
Cogito: automated and generic comparison of annotated genomic intervals. 315 - Kolja Thormann
ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures. 316 - Sierra S. Nishizaki
SEMplMe: a tool for integrating DNA methylation effects in transcription factor binding affinity predictions. 317 - Yi Yue, Chen Ye, Pei-Yun Peng, Hui-Xin Zhai, Iftikhar Ahmad, Chuan Xia, Yun-Zhi Wu, You-Hua Zhang:
A deep learning framework for identifying essential proteins based on multiple biological information. 318 - Subhadip Saha
In-silico design of an immunoinformatics based multi-epitope vaccine against Leishmania donovani. 319 - Birbal Prasad, Xinzhong Li:
Fused inverse-normal method for integrated differential expression analysis of RNA-seq data. 320 - Shrabanti Chowdhury
DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer. 321 - Yawu Zhao
CRANet: a comprehensive residual attention network for intracranial aneurysm image classification. 322 - Nada Al taweraqi, Ross D. King:
Improved prediction of gene expression through integrating cell signalling models with machine learning. 323 - Asier Antoranz
ELIMINATOR: essentiality analysis using multisystem networks and integer programming. 324 - Kah Yee Tai, Jasbir Dhaliwal, KokSheik Wong
Risk score prediction model based on single nucleotide polymorphism for predicting malaria: a machine learning approach. 325 - Nadav S. Bar, Bahareh Nikparvar, Naresh Doni Jayavelu, Fabienne Krystin Roessler:
Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions. 330 - Morteza Kouhsar, Esra Kashaninia, Behnam Mardani, Hamid R. Rabiee:
CircWalk: a novel approach to predict CircRNA-disease association based on heterogeneous network representation learning. 331 - Afifa Khaled, Jian-Jun Han, Taher Ahmed Ghaleb:
Learning to detect boundary information for brain image segmentation. 332 - Shao-Wu Zhang, Zhen-Nan Wang, Yan Li, Weifeng Guo
Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network. 341 - Heewon Park, Seiya Imoto, Satoru Miyano:
PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. 342 - Judah Zammit, Daryl L. X. Fung, Qian Liu, Carson Kai-Sang Leung
Semi-supervised COVID-19 CT image segmentation using deep generative models. 343 - Mario Grassi, Barbara Tarantino
SEMgsa: topology-based pathway enrichment analysis with structural equation models. 344 - Wei Li, Lina Yang, Yu Qiu, Yujian Yuan, Xichun Li, Zuqiang Meng:
FFP: joint Fast Fourier transform and fractal dimension in amino acid property-aware phylogenetic analysis. 347 - Sandra Hui
SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances. 348 - Niraj Thapa, Meenal Chaudhari, Sean McManus, Kaushik Roy, Robert H. Newman
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. 349 - Linrong Li
High expression of cuproptosis-related SLC31A1 gene in relation to unfavorable outcome and deregulated immune cell infiltration in breast cancer: an analysis based on public databases. 350 - Anna Pacínková, Vlad Popovici
Using empirical biological knowledge to infer regulatory networks from multi-omics data. 351 - Yinchao Fei, Hao Zhang
LTPConstraint: a transfer learning based end-to-end method for RNA secondary structure prediction. 354 - Dingqin He, Ming Chen, Wenjuan Wang, Chunhui Song, Yufang Qin:
Deconvolution of tumor composition using partially available DNA methylation data. 355 - Su Wang
Evaluation of vicinity-based hidden Markov models for genotype imputation. 356 - Sangyeol Kim, Seongjun Park, Iksoo Chang:
Development of quantitative and continuous measure for severity degree of Alzheimer's disease evaluated from MRI images of 761 human brains. 357 - Chuangye Song, Jiawen Sang, Lin Zhang, Huiming Liu, Dongxiu Wu, Weiying Yuan, Chong Huang:
Adaptiveness of RGB-image derived algorithms in the measurement of fractional vegetation coverage. 358 - Zhonghe Shao, Ting Wang, Jiahao Qiao, Yuchen Zhang, Shuiping Huang, Ping Zeng:
A comprehensive comparison of multilocus association methods with summary statistics in genome-wide association studies. 359 - Noushin Hajarolasvadi
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks. 360 - David Chardin, Cyprien Gille
Learning a confidence score and the latent space of a new supervised autoencoder for diagnosis and prognosis in clinical metabolomic studies. 361 - Feng Yang, Juan Liu, Qiang Zhang, Zhihui Yang, Xiaolei Zhang:
CNN-based two-branch multi-scale feature extraction network for retrosynthesis prediction. 362 - Jens Uwe Loers, Vanessa Vermeirssen:
SUBATOMIC: a SUbgraph BAsed mulTi-OMIcs clustering framework to analyze integrated multi-edge networks. 363 - Leroy Bondhus
DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. 364 - Fanny Mollandin
Accounting for overlapping annotations in genomic prediction models of complex traits. 365 - Changyong Yu, Pengxi Lin, Yuhai Zhao, Tianmei Ren, Guoren Wang:
A fast and efficient path elimination algorithm for large-scale multiple common longest sequence problems. 366 - Shaofu Lin, Chengyu Shi, Jianhui Chen:
GeneralizedDTA: combining pre-training and multi-task learning to predict drug-target binding affinity for unknown drug discovery. 367 - Chenran Wang, Yang Chen, Yuan Zhang
A reinforcement learning approach for protein-ligand binding pose prediction. 368 - Mohammad Taheri-Ledari
Assignment of structural domains in proteins using diffusion kernels on graphs. 369 - Mayank Baranwal, Abram Magner, Jacob Saldinger, Emine Sumeyra Turali-Emre
Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions. 370 - Osamu Maruyama, Yinuo Li, Hiroki Narita, Hidehiro Toh
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers. 371 - Fan Zhang, Wei Hu, Yirong Liu:
GCMM: graph convolution network based on multimodal attention mechanism for drug repurposing. 372 - Zhenyu Wei, Qi Cheng
Investigation of CRS-associated cytokines in CAR-T therapy with meta-GNN and pathway crosstalk. 373 - Minji Jeon, Zhuorui Xie, John Erol Evangelista, Megan L. Wojciechowicz, Daniel J. B. Clarke
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. 374 - Juan O. Lopez
Pattern matching for high precision detection of LINE-1s in human genomes. 375 - Anna Pacínková, Vlad Popovici:
Correction: Using empirical biological knowledge to infer regulatory networks from multi-omics data. 376 - Alexei A. Sharov, Yuhki Nakatake, Weidong Wang:
Atlas of regulated target genes of transcription factors (ART-TF) in human ES cells. 377 - Rohan Subramanian, Debashis Sahoo:
Boolean implication analysis of single-cell data predicts retinal cell type markers. 378 - Mathias Gotsmy
Probabilistic quotient's work and pharmacokinetics' contribution: countering size effect in metabolic time series measurements. 379 - Elham Bayat Mokhtari, Benjamin Jerry Ridenhour:
Filtering ASVs/OTUs via mutual information-based microbiome network analysis. 380 - He-Ming Chu, Jin-Xing Liu, Ke Zhang, Chun-Hou Zheng, Juan Wang, Xiang-Zhen Kong:
A binary biclustering algorithm based on the adjacency difference matrix for gene expression data analysis. 381 - Yue Gao, Songling Chen
Topology-enhanced molecular graph representation for anti-breast cancer drug selection. 382 - Heesun Kim, Mikang Sim, Na Young Park
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. 383 - Dmitry Evgenevich Mylarshchikov
ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs. 384 - Xiang Li, Zeng Li, Shanzhi Gu, Xinhan Zhao:
A pan-cancer analysis of collagen VI family on prognosis, tumor microenvironment, and its potential therapeutic effect. 390 - AmirHosein Sadeghimanesh
Polynomial superlevel set representation of the multistationarity region of chemical reaction networks. 391 - Petr Rysavý
circGPA: circRNA functional annotation based on probability-generating functions. 392 - Bilin Liang, Haifan Gong, Lu Lu
Risk stratification and pathway analysis based on graph neural network and interpretable algorithm. 394 - Sonja Zehetmayer
Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments. 388 - E. C. Wood, Amy Glen
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. 400 - Tommaso Alfonsi
Genomic data integration and user-defined sample-set extraction for population variant analysis. 401 - Jiaqing Lyu, Zhen Yao, Bing Liang, Yiwei Liu, Yijia Zhang:
Small protein complex prediction algorithm based on protein-protein interaction network segmentation. 405 - Wei Liu
Oxidative stress genes in patients with esophageal squamous cell carcinoma: construction of a novel prognostic signature and characterization of tumor microenvironment infiltration. 406 - Miran Kim, Su Wang
SVAT: Secure outsourcing of variant annotation and genotype aggregation. 409 - Eskandar Taghizadeh, Sahel Heydarheydari, Alihossein Saberi, Shabnam JafarpoorNesheli, Seyed Masoud Rezaeijo:
Breast cancer prediction with transcriptome profiling using feature selection and machine learning methods. 410 - Qing Yang, Sunan Gao
A machine learning-based data mining in medical examination data: a biological features-based biological age prediction model. 411 - Yingxia Li
Benchmark study of feature selection strategies for multi-omics data. 412 - Victor Akpokiro, Trevor Martin, Oluwatosin Oluwadare
EnsembleSplice: ensemble deep learning model for splice site prediction. 413 - Rongquan Wang, Caixia Wang
Detecting protein complexes with multiple properties by an adaptive harmony search algorithm. 414 - Yiru Sheng, R. Ayesha Ali, Andreas Heyland
Comparative transcriptomics analysis pipeline for the meta-analysis of phylogenetically divergent datasets (CoRMAP). 415 - Josh Harling-Lee
A graph-based approach for the visualisation and analysis of bacterial pangenomes. 416 - Jing Tian, Mingzhen Zhu, Zijing Ren, Qiang Zhao, Puqing Wang, Colin K. He, Min Zhang, Xiaochun Peng, Beilei Wu, Rujia Feng, Minglong Fu:
Deep learning algorithm reveals two prognostic subtypes in patients with gliomas. 417 - Rui Zhou
Novel six-gene prognostic signature based on colon adenocarcinoma immune-related genes. 418 - Josh L. Espinoza, Chris L. Dupont:
VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes. 419 - Zhuoran Ding, Marylyn D. Ritchie, Benjamin F. Voight
Estimating the effect size of a hidden causal factor between SNPs and a continuous trait: a mediation model approach. 420 - Camille Clouard
A joint use of pooling and imputation for genotyping SNPs. 421 - Saeid Azadifar, Ali Ahmadi:
A novel candidate disease gene prioritization method using deep graph convolutional networks and semi-supervised learning. 422 - Fan Yang, Jian Zhang, Wanyi Chen, Yongxuan Lai, Ying Wang, Quan Zou:
DeepMPM: a mortality risk prediction model using longitudinal EHR data. 423 - James G. Mann, R. Jason Pitts:
PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs. 428 - Surabhi Jagtap
BRANEnet: embedding multilayer networks for omics data integration. 429 - Jiquan Shen, Jiawei Shi, Junwei Luo, Haixia Zhai, Xiaoyan Liu, Zhengjiang Wu, Chaokun Yan, Huimin Luo:
Deep learning approach for cancer subtype classification using high-dimensional gene expression data. 430 - Joyce Zhanzi Wang
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review. 431 - Ruiyu Guo, Hailin Chen
Predicting potential miRNA-disease associations based on more reliable negative sample selection. 432 - Yang Yang, Zhouyao Qian, Mingyang Feng
Study on the prognosis, immune and drug resistance of m6A-related genes in lung cancer. 437 - Chengkai Piao, Mengyue Lv, Shujie Wang, Rongyan Zhou, Yuchen Wang, Jinmao Wei, Jian Liu:
Multi-objective data enhancement for deep learning-based ultrasound analysis. 438 - Alexia Akalestou-Clocher, Vivian Kalamara, Pantelis Topalis, George A. Garinis
SpotitPy: a semi-automated tool for object-based co-localization of fluorescent labels in microscopy images. 439 - Rajendra Kumar Gurumurthy, Klaus-Peter Pleissner, Cindrilla Chumduri
Single object profiles regression analysis (SOPRA): a novel method for analyzing high-content cell-based screens. 440 - Amrita Chattopadhyay, Ching-Yu Shih, Yu-Chen Hsu, Jyh-Ming Jimmy Juang, Eric Y. Chuang, Tzu-Pin Lu
CLIN_SKAT: an R package to conduct association analysis using functionally relevant variants. 441 - Roeland E. Voorrips
PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. 442 - Mykyta Matushyn
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration. 443 - Lin Zhu, Xiaoyu Wang, Fuyi Li
PreAcrs: a machine learning framework for identifying anti-CRISPR proteins. 444 - Oscar A. Zarate, Yiben Yang, Xiaozhong Wang, Ji-Ping Wang:
BoostMEC: predicting CRISPR-Cas9 cleavage efficiency through boosting models. 446 - Lun Hu, Zhenfeng Li, Zehai Tang, Cheng Zhao, Xi Zhou, Pengwei Hu:
Effectively predicting HIV-1 protease cleavage sites by using an ensemble learning approach. 447 - Augustin Boudry, Sasha Darmon, Nicolas Duployez
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. 448 - Corey Weistuch, Jiening Zhu, Joseph O. Deasy
The maximum entropy principle for compositional data. 449 - Jianhua Jia, Genqiang Wu
pSuc-EDBAM: Predicting lysine succinylation sites in proteins based on ensemble dense blocks and an attention module. 450 - Ruiming Li, Jung-Yu Lee, Jinn-Moon Yang, Tatsuya Akutsu:
Densest subgraph-based methods for protein-protein interaction hot spot prediction. 451 - Arun Das, Michael C. Schatz:
Sketching and sampling approaches for fast and accurate long read classification. 452 - Bei Hong, Jing Liu, Hao Zhai
Joint reconstruction of neuron and ultrastructure via connectivity consensus in electron microscope volumes. 453 - Sangjeong Lee, Heejin Park, Hyunwoo Kim
False discovery rate estimation using candidate peptides for each spectrum. 454 - Kazuhiro Maeda
MLAGO: machine learning-aided global optimization for Michaelis constant estimation of kinetic modeling. 455 - Lin Gu, Bin Li, Dengming Ming:
A multilayer dynamic perturbation analysis method for predicting ligand-protein interactions. 456 - Ta-Chun Liu, Peter N. Kalugin
GMMchi: gene expression clustering using Gaussian mixture modeling. 457 - Zhiyu Zhang, Arbee L. P. Chen:
Biomedical named entity recognition with the combined feature attention and fully-shared multi-task learning. 458 - Hongmei Wang, Fang Guo, Mengyan Du, Guishen Wang
A novel method for drug-target interaction prediction based on graph transformers model. 459 - Hui Li, Davis J. McCarthy, Heejung Shim
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics. 460 - Sylwan Rahardja, Mou Wang
A lightweight classification of adaptor proteins using transformer networks. 461 - Nathan P. Gill, Raji Balasubramanian, James R. Bain
Correction: Path-level interpretation of Gaussian graphical models using the pair-path subscore. 462 - Sean Higgins, Victor Akpokiro, Allen Westcott, Oluwatosin Oluwadare
TADMaster: a comprehensive web-based tool for the analysis of topologically associated domains. 463 - Roberto R. Expósito
SparkEC: speeding up alignment-based DNA error correction tools. 464 - Yekai Zhou
Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing. 465 - Emmanuel Onah
Prediction of HIV-1 protease cleavage site from octapeptide sequence information using selected classifiers and hybrid descriptors. 466 - Jingmin An, Xiaogang Weng:
Collectively encoding protein properties enriches protein language models. 467 - Kuncheng Song
C3NA: correlation and consensus-based cross-taxonomy network analysis for compositional microbial data. 468 - Younghoon Kim, Tao Wang, Danyi Xiong, Xinlei Wang, Seongoh Park:
Multiple instance neural networks based on sparse attention for cancer detection using T-cell receptor sequences. 469 - Zhenzhen Xue, Cheng Li, Zhuo-Ming Luo, Shan-Shan Wang, Ying-Ying Xu:
Automated classification of protein expression levels in immunohistochemistry images to improve the detection of cancer biomarkers. 470 - Hao Yang, Jiaxi Li, Siru Liu, Mengjiao Zhang, Jialin Liu:
An interpretable DIC risk prediction model based on convolutional neural networks with time series data. 471 - Zhenlei Li, Ya Huang, Qingrun Li, Yidi Sun, Chen Li, Jiarui Wu, Haoran Zheng, Rong Zeng:
TreeQNet: a webserver for Treatment evaluation with Quantified Network. 473 - Lorenzo Di Rocco, Umberto Ferraro Petrillo, Simona E. Rombo
DIAMIN: a software library for the distributed analysis of large-scale molecular interaction networks. 474 - Tobias Wängberg, Joanna Tyrcha, Chun-Biu Li:
Shape-aware stochastic neighbor embedding for robust data visualisations. 477 - Peixin Tian, Yiqian Hu, Zhonghua Liu, Yan Dora Zhang:
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures. 478 - Xuanfeng Zhang, Dong Zhang, Xuefeng Bu, Xinhui Zhang, Long Cui:
Identification of a novel miRNA-based recurrence and prognosis prediction biomarker for hepatocellular carcinoma. 479 - Meng Liao, Jian-ping Zhao, Jing Tian, Chun-Hou Zheng:
iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework. 480 - Cecilia Wieder
Single sample pathway analysis in metabolomics: performance evaluation and application. 481 - Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir, Aaron R. Quinlan:
Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. 482 - Jian Guan, Zhao Gong Zhang, Yong Liu, Meng Wang:
A novel bi-directional heterogeneous network selection method for disease and microbial association prediction. 483 - Li Zhang, Jingwei Xu, Xiufeng Chu, Hongqiao Zhang, Xueyuan Yao, Jian Zhang, Yanwei Guo:
Identification of the cuproptosis-related molecular subtypes and an immunotherapy prognostic model in hepatocellular carcinoma. 485 - Eun Byul Lee, Go Eun Heo, Chang Min Choi, Min Song:
MLM-based typographical error correction of unstructured medical texts for named entity recognition. 486 - Jan Verhoeff
INFLECT: an R-package for cytometry cluster evaluation using marker modality. 487 - Igor V. Deyneko
Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes. 488 - Brian Vestal
lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models. 489 - Thomas J. Nicholas
Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. 490 - Yaqin Tan, Juan Zou, Linai Kuang, Xiangyi Wang, Bin Zeng, Zhen Zhang, Lei Wang:
GSAMDA: a computational model for predicting potential microbe-drug associations based on graph attention network and sparse autoencoder. 492 - Sai Hu, Yingchun Luo, Zhihong Zhang, Hui-jun Xiong, Wei Yan, Meiping Jiang, Bihai Zhao:
Protein function annotation based on heterogeneous biological networks. 493 - Rongquan Wang, Caixia Wang, Huimin Ma:
Correction: Detecting protein complexes with multiple properties by an adaptive harmony search algorithm. 494 - Matthias Zytnicki, Christine Gaspin:
srnaMapper: an optimal mapping tool for sRNA-Seq reads. 495 - Abdu Rehaman Pasha Syed, Rahul Anbalagan, Anagha S. Setlur
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers. 496 - Xuewen Wang
USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences. 497 - Jean-Tristan Brandenburg
H3AGWAS: a portable workflow for genome wide association studies. 498 - Adrien Vidal
SeSAM: software for automatic construction of order-robust linkage maps. 499 - Akio Miyao
Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. 500 - Xiangwen Zheng, Haijian Du, Xiaowei Luo
BioByGANS: biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework. 501 - Keith Noto, Luong Ruiz:
Accurate genome-wide phasing from IBD data. 502 - Guo Mao, Ruigeng Zeng, Jintao Peng, Ke Zuo, Zhengbin Pang, Jie Liu:
Reconstructing gene regulatory networks of biological function using differential equations of multilayer perceptrons. 503 - Chengyang Ji
sitePath: a visual tool to identify polymorphism clades and help find fixed and parallel mutations. 504 - C. Nicholas Henry, Kathryn Piper, Amanda E. Wilson, John L. Miraszek, Claire S. Probst, Yuying Rong
WGDTree: a phylogenetic software tool to examine conditional probabilities of retention following whole genome duplication events. 505 - Aravind Ashok Nair, Helena Arvidsson, Jorge E. Gatica V., Nikolce Tudzarovski, Karl Meinke, Rachael V. Sugars
A graph neural network framework for mapping histological topology in oral mucosal tissue. 506 - Ankit Gupta
MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets. 507 - Rira Matsuta, Hiroyuki Yamamoto, Masaru Tomita, Rintaro Saito:
iDMET: network-based approach for integrating differential analysis of cancer metabolomics. 508 - Yuridia S. Posadas-García
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. 509 - Veronica Gheorghe
Optimal construction of a functional interaction network from pooled library CRISPR fitness screens. 510 - Muhammad Muneeb, Samuel F. Feng, Andreas Henschel:
Transfer learning for genotype-phenotype prediction using deep learning models. 511 - Gustavo Tamasco
ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization. 512 - Jingchao Sun, Zhining Qiu, Rob Egan, Harrison Ho
Persistent memory as an effective alternative to random access memory in metagenome assembly. 513 - Marta Moreno
Scalable transcriptomics analysis with Dask: applications in data science and machine learning. 514 - Minsoo Kim
Mathematical model of the cell signaling pathway based on the extended Boolean network model with a stochastic process. 515 - Menglong Zhang, Bo-Wei Zhao, Xiao-Rui Su, Yi-Zhou He, Yue Yang, Lun Hu:
RLFDDA: a meta-path based graph representation learning model for drug-disease association prediction. 516 - Alessia Auriemma Citarella
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier. 517 - Miquel Anglada-Girotto
robustica: customizable robust independent component analysis. 519 - Hocheol Lim, Kyoung Tai No:
Prediction of polyreactive and nonspecific single-chain fragment variables through structural biochemical features and protein language-based descriptors. 520 - Wen Zhong, Changxiang He, Chen Xiao, Yuru Liu, Xiaofei Qin, Zhensheng Yu:
Long-distance dependency combined multi-hop graph neural networks for protein-protein interactions prediction. 521 - Dovydas Kiciatovas, Qingli Guo, Miika Kailas, Henri Pesonen, Jukka Corander, Samuel Kaski, Esa Pitkänen
Identification of multiplicatively acting modulatory mutational signatures in cancer. 522 - Yun Jiang, Zeqi Ma, Chao Wu, Zequn Zhang, Wei Yan:
RSAP-Net: joint optic disc and cup segmentation with a residual spatial attention path module and MSRCR-PT pre-processing algorithm. 523 - Thuy Trang Dinh, Trang Phuong Vo-Chanh, Chau Nguyen, Viet Quoc Huynh, Nam Vo
Extract antibody and antigen names from biomedical literature. 524 - Wei Jiang
An unbiased kinship estimation method for genetic data analysis. 525 - Sen Wang, Hengchao Wang
EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends. 528 - Tiana Fitzgerald, Andrew Jones, Barbara E. Engelhardt
A Poisson reduced-rank regression model for association mapping in sequencing data. 529 - Sebastian Reinhard
ReCSAI: recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy. 530 - Felix Nikolaus Wirth
EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation. 531 - Augustin Boudry, Sasha Darmon, Nicolas Duployez
Publisher Correction: Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. 533 - Metoboroghene Oluwaseyi Mowoe, Shaun Garnett, Katherine Lennard, Jade Talbot, Paul Townsend, Eduard Jonas, Jonathan M. Blackburn
Pro-MAP: a robust pipeline for the pre-processing of single channel protein microarray data. 534 - Xiaowei Wu, Shicheng Liu, Guanying Liang:
Detecting clusters of transcription factors based on a nonhomogeneous poisson process model. 535 - Fu Xiang Quah
SC3s: efficient scaling of single cell consensus clustering to millions of cells. 536 - Jero Mario Schäfer
Graph4Med: a web application and a graph database for visualizing and analyzing medical databases. 537 - Grzegorz Mrukwa, Joanna Polanska
DiviK: divisive intelligent K-means for hands-free unsupervised clustering in big biological data. 538 - Lifei Wang, Rui Nie, Jiang Zhang, Jun Cai:
scCapsNet-mask: an updated version of scCapsNet with extended applicability in functional analysis related to scRNA-seq data. 539 - Markus Viljanen, Hendriek C. Boshuizen:
llperm: a permutation of regressor residuals test for microbiome data. 540 - Daniel M. Portik, C. Titus Brown, N. Tessa Pierce-Ward
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. 541 - Natasha N. Kunchur, Leila B. Mostaço-Guidolin:
Development of an image classification pipeline for atherosclerotic plaques assessment using supervised machine learning. 542 - Jialin Wu, Zhe Liu, Xiaofeng Yang, Zhanglin Lin:
Improved compound-protein interaction site and binding affinity prediction using self-supervised protein embeddings. 543 - Trinity Cheng, Pei-Ju Chin
Profiling the BLAST bioinformatics application for load balancing on high-performance computing clusters. 544 - Eleni Adam, Desh Ranjan, Harold Riethman:
NPGREAT: assembly of human subtelomere regions with the use of ultralong nanopore reads and linked-reads. 545 - Benedek Bozoky
AtlasGrabber: a software facilitating the high throughput analysis of the human protein atlas online database. 546 - Alejandro Cisterna
PhenoExam: gene set analyses through integration of different phenotype databases. 567 - Katarzyna Nalecz-Charkiewicz, Robert M. Nowak:
Algorithm for DNA sequence assembly by quantum annealing. 122 - Simone Pallotta, Silvia Cascianelli
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor. 123 - Zhiqiao Zhang, Liwen Huang, Jing Li, Peng Wang:
Bioinformatics analysis reveals immune prognostic markers for overall survival of colorectal cancer patients: a novel machine learning survival predictive system. 124 - Zhaoyi Zhang, Songyang Cheng, Claudia R. Solís-Lemus
Towards a robust out-of-the-box neural network model for genomic data. 125 - Liyi Yu, Wangren Qiu, Weizhong Lin, Xiang Cheng, Xuan Xiao, Jiexia Dai:
HGDTI: predicting drug-target interaction by using information aggregation based on heterogeneous graph neural network. 126 - Emre Sefer
A comparison of topologically associating domain callers over mammals at high resolution. 127 - Paolo Inglese, Helen Xuexia Huang
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions. 133 - Emanuele Marchi, Mathew Jones, Paul Klenerman, John Frater
BreakAlign: a Perl program to align chimaeric (split) genomic NGS reads and allow visual confirmation of novel retroviral integrations. 134 - Ying Li, Lizheng Wei, Cankun Wang
LPInsider: a webserver for lncRNA-protein interaction extraction from the literature. 135 - Li Zhang, Xiaoran Yang, Shijian Li, Tianyi Liao, Gang Pan:
Answering medical questions in Chinese using automatically mined knowledge and deep neural networks: an end-to-end solution. 136 - Jody Phelan
COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data. 137 - Hamed Dashti, Iman Dehzangi
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. 138 - Sebastian Winkler
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. 139 - Anni A. Antikainen
Modeling binding specificities of transcription factor pairs with random forests. 212 - Tiantian Liu, Chao Zhou, Huimin Wang, Hongyu Zhao
phyloMDA: an R package for phylogeny-aware microbiome data analysis. 213 - Sebastian Raubach
GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization. 214 - Shanliang Zhong, Jifeng Feng
CircPrimer 2.0: a software for annotating circRNAs and predicting translation potential of circRNAs. 215 - Tristan Dubos, Axel Poulet
NODeJ: an ImageJ plugin for 3D segmentation of nuclear objects. 216 - Michael Bernhofer, Burkhard Rost
TMbed: transmembrane proteins predicted through language model embeddings. 326 - Chen Gao, Ning Kong, Fan Zhang, Liuzhi Zhou, Maosheng Xu, Linyu Wu
Development and validation of the potential biomarkers based on m6A-related lncRNAs for the predictions of overall survival in the lung adenocarcinoma and differential analysis with cuproptosis. 327 - M. E. Nelson, Simone G. Riva, Ana Cvejic:
SMaSH: a scalable, general marker gene identification framework for single-cell RNA-sequencing. 328 - Yixiang Zhang, Kent M. Eskridge, Shunpu Zhang, Guoqing Lu:
Identifying host-specific amino acid signatures for influenza A viruses using an adjusted entropy measure. 333 - Daniel Wüstner
Image segmentation and separation of spectrally similar dyes in fluorescence microscopy by dynamic mode decomposition of photobleaching kinetics. 334 - Nono S. C. Merleau
aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights. 335 - Mariia Bilous, Loc Tran, Chiara Cianciaruso, Aurélie Gabriel, Hugo Michel, Santiago J. Carmona, Mikael J. Pittet
Metacells untangle large and complex single-cell transcriptome networks. 336 - Xingang Jia
Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features. 337 - Susanna R. Grigson
Organizing the bacterial annotation space with amino acid sequence embeddings. 385 - Xiaoxia Wen, Ping Leng, Jiasi Wang, Guishu Yang, Ruiling Zu, Xiaojiong Jia, Kaijiong Zhang, Birga Anteneh Mengesha, Jian Huang
Clinlabomics: leveraging clinical laboratory data by data mining strategies. 387 - Milad Salem, Arash Keshavarzi Arshadi, Jiann-Shiun Yuan:
AMPDeep: hemolytic activity prediction of antimicrobial peptides using transfer learning. 389 - Juntao Li
Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression. 434 - Zezhou Hao, Pengchen Liang
Prognostic risk assessment model and drug sensitivity analysis of colon adenocarcinoma (COAD) based on immune-related lncRNA pairs. 435 - Jacob Williams, Marco A. R. Ferreira, Tieming Ji:
BICOSS: Bayesian iterative conditional stochastic search for GWAS. 475 - Abbas Rammal, Rabih Assaf, Alban Goupil, Mohammad Kacim, Valeriu Vrabie:
Machine learning techniques on homological persistence features for prostate cancer diagnosis. 476 - Guy Shtar, Asnat Greenstein-Messica, Eyal Mazuz, Lior Rokach, Bracha Shapira
Predicting drug characteristics using biomedical text embedding. 526 - Hongya Zhang, Xuexiang Li, Tianying Zhang, Qianhui Zhou, Cong Zhang:
Establishment and validation of a predictive model of preeclampsia based on transcriptional signatures of 43 genes in decidua basalis and peripheral blood. 527 - Georg Hahn, Sanghun Lee, Dmitry Prokopenko, Jonathan Abraham, Tanya Novak, Julian Hecker, Michael H. Cho, Surender Khurana, Lindsey R. Baden, Adrienne G. Randolph, Scott T. Weiss, Christoph Lange:
Unsupervised outlier detection applied to SARS-CoV-2 nucleotide sequences can identify sequences of common variants and other variants of interest. 547 - Kai Guo, Xiongfei Li, Tie-hu Fan, Xiaohan Hu:
VANet: a medical image fusion model based on attention mechanism to assist disease diagnosis. 548 - Kai He, Rui Mao
JCBIE: a joint continual learning neural network for biomedical information extraction. 549 - Dustin Kenefake, Erick Armingol, Nathan E. Lewis
An improved algorithm for flux variability analysis. 550 - Askar Gafurov
VirPool: model-based estimation of SARS-CoV-2 variant proportions in wastewater samples. 551 - Shaofu Lin, Mengzhen Wang, Chengyu Shi, Zhe Xu, Lihong Chen, Qingcai Gao, Jianhui Chen:
MR-KPA: medication recommendation by combining knowledge-enhanced pre-training with a deep adversarial network. 552 - Yaru Hao, Xiao-Yuan Jing, Qixing Sun:
Joint learning sample similarity and correlation representation for cancer survival prediction. 553 - Eman Ismail, Walaa K. Gad, Mohamed Hashem:
HEC-ASD: a hybrid ensemble-based classification model for predicting autism spectrum disorder disease genes. 554 - Amina Bedrat
UGDR: a generic pipeline to detect recombined regions in polyploid and complex hybrid yeast genomes. 555 - Abhisek Tiwari, Tulika Saha, Sriparna Saha, Pushpak Bhattacharyya, Shemim Begum, Minakshi Dhar
Symptoms are known by their companies: towards association guided disease diagnosis assistant. 556 - Xuedong Wang, Yanle Liu, Xinyao Miao
Correction: DENSEN: a convolutional neural network for estimating chronological ages from panoramic radiographs. 557 - Antonella Dellanzo, Viviana Cotik, Daniel Yunior Lozano Barriga, Jonathan Jimmy Mollapaza Apaza, Daniel Palomino, Fernando Schiaffino, Alexander Yanque Aliaga, José Ochoa Luna:
Digital surveillance in Latin American diseases outbreaks: information extraction from a novel Spanish corpus. 558 - Dingkai Huang, Hongjian He, Jiaming Ouyang, Chang Zhao, Xin Dong, Jiang Xie:
Small molecule drug and biotech drug interaction prediction based on multi-modal representation learning. 561 - Jin-xiao Liang, Qian Chen, Wei Gao, Da Chen, Xin-yu Qian, Jin-qiao Bi, Xing-chen Lin, Bing-bing Han, Jin-shi Liu:
A novel glycosylation-related gene signature predicts survival in patients with lung adenocarcinoma. 562 - Xin Wang, Yadong Liu, Jie Li, Guohua Wang:
StackCirRNAPred: computational classification of long circRNA from other lncRNA based on stacking strategy. 563 - Junjun Zhang, Minzhu Xie:
Graph regularized non-negative matrix factorization with prior knowledge consistency constraint for drug-target interactions prediction. 564 - José Antonio Barbero-Aparicio
Nonlinear physics opens a new paradigm for accurate transcription start site prediction. 565 - Max van 't Hof
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. 566 - Abdullah Soydan Mahmutoglu
The effect of radiofrequency ablation on pain score and non-steroidal painkiller use in osteoid osteoma patients. 160 - Liping Yang, Xing Gao, Chao Gao, Shichuan Xu, Shaodong Cao:
Dynamic evaluation of unruptured intracranial aneurysms by 4D-CT angiography: comparison with digital subtraction angiography (DSA) and surgical findings. 161 - Naga Raju Gudhe, Veli-Matti Kosma, Hamid Behravan, Arto Mannermaa:
Nuclei instance segmentation from histopathology images using Bayesian dropout based deep learning. 162 - Jiyun Chen, Xijun Zhang, Jianjun Yuan, Renjie Shao, Conggui Gan, Qiang Ji, Wei Luo, Zhi-Feng Pang
Weakly supervised video-based cardiac detection for hypertensive cardiomyopathy. 163 - Sang Won Jo
Changes in radiomic and radiologic features in meningiomas after radiation therapy. 164 - Mohammad Mehdi Baradaran Mahdavi, Mehravar Rafati, Mostafa Ghanei, Masoud Arabfard:
Computer-assisted evaluation of small airway disease in CT scans of Iran-Iraq war victims of chemical warfare by a locally developed software: comparison between different quantitative methods. 165 - Min Wang, Jiayu Zhang, Jiao Ma, Liyi Liu, Jia Wang, Chunyin Zhang:
Imaging findings and clinical relevance of 68Ga-Pentixafor PET in atherosclerosis: a systematic review. 166 - Xin-Yue Yan, Hai-Yue Ju, Fang-Jing Hou, Xiao-Ting Li, Ding Yang, Lei Tang, Ya-Kun Wang, Zhong-Wu Li, Ying-Shi Sun, Shun-Yu Gao:
Analysis of enhanced CT imaging signs and clinicopathological prognostic factors in hepatoid adenocarcinoma of stomach patients with radical surgery: a retrospective study. 167 - Xiuzhen Yao, Weiqun Ao, Xiandi Zhu, Shuyuan Tian, Xiaoyu Han, Jinwen Hu, Wenjie Xu, Guoqun Mao, Shuitang Deng:
A novel radiomics based on multi-parametric magnetic resonance imaging for predicting Ki-67 expression in rectal cancer: a multicenter study. 168 - Feifei Xia, Foqing Guo, Zhe Liu, Jie Zeng, Xuehua Ma, Chongqing Yu, Changxue Li:
Enhanced CT combined with texture analysis for differential diagnosis of pleomorphic adenoma and adenolymphoma. 169
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