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ORCIDBMC 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
:
Sensei: how many samples to tell a change in cell type abundance? 2 - Laurent S. V. Thomas, Jochen Gehrig:
Correction to: Multi-template matching: a versatile tool for object-localization in microscopy images. 3 - Aparna Elangovan, Yuan Li, Douglas E. V. Pires, Melissa J. Davis, Karin Verspoor:
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, Fereshteh Mataeimoghadam, Rianon Zaman, Abdul Sattar:
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, Michael J. Muehlbauer, William L. Lowe Jr., Denise M. Scholtens:
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, Zalak V. Shah, Katie R. Bradwell, James B. Munro, Andrea A. Berry, David Serre, Shannon Takala-Harrison, Timothy D. O'Connor, Joana C. Silva, Mark A. Travassos:
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. 15 - Huijian Feng, Lihui Lin, Jiekai Chen:
scDIOR: single cell RNA-seq data IO software. 16 - Tulika Kakati, Dhruba K. Bhattacharyya, Jugal K. Kalita, Trina M. Norden-Krichmar:
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning. 17 - Jörg Winkler, Gianvito Urgese, Elisa Ficarra, Knut Reinert:
LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences. 18 - Junhui Qiu, Qi Zhou, Weicai Ye, Qianjun Chen, Yun-Juan Bao:
SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes. 19 - Jing Chen, Baotian Hu, Weihua Peng, Qingcai Chen, Buzhou Tang:
Biomedical relation extraction via knowledge-enhanced reading comprehension. 20 - Julia Vetter, Susanne Schaller, Andreas Heinzel, Constantin Aschauer, Roman Reindl-Schwaighofer, Kira Jelencsics, Karin Hu, Rainer Oberbauer, Stephan M. Winkler:
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data. 21 - Vi Ngoc-Nha Tran, Alireza Shams, Sinan Ascioglu, Antal Martinecz, Jingyi Liang, Fabrizio Clarelli, Rafal Mostowy, Ted Cohen, Pia Abel zur Wiesch:
vCOMBAT: a novel tool to create and visualize a computational model of bacterial antibiotic target-binding. 22 - Juan J. Lastra-Díaz, Alicia Lara-Clares, Ana García-Serrano:
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, Anne Buu:
Polygenic risk prediction based on singular value decomposition with applications to alcohol use disorder. 28 - Xifang Sun, Donglin Wang, Jiaqiang Zhu, Shiquan Sun:
A novel nonparametric computational strategy for identifying differential methylation regions. 29 - Xiong Yuan, Zirong Li, Liwen Xiong, Sufeng Song, Xingfei Zheng, Zhonghai Tang, Zheming Yuan, Lanzhi Li:
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, Manuela Zucknick, Katja Ickstadt, Jörg Rahnenführer:
Correction to: Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression. 32 - Lakshay Anand, Carlos M. Rodriguez Lopez:
ChromoMap: an R package for interactive visualization of multi-omics data and annotation of chromosomes. 33 - Fei Song, Shiyin Tan, Zengfa Dou, Xiaogang Liu, Xiaoke Ma:
Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks. 34 - Miaoshan Lu, Shaowei An, Ruimin Wang, Jinyin Wang, Changbin Yu:
Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time. 35 - Lucille Lopez-Delisle, Jean-Baptiste 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, Parvin Mousavi:
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, Kathrin M. Seibt, Beatrice Weber, Tony Heitkam:
ECCsplorer: a pipeline to detect extrachromosomal circular DNA (eccDNA) from next-generation sequencing data. 40 - Maia H. Malonzo, Viivi Halla-aho, Mikko Konki, Riikka J. Lund, Harri Lähdesmäki:
LuxRep: a technical replicate-aware method for bisulfite sequencing data analysis. 41 - Mehrdad Mansouri, Sahand Khakabimamaghani, Leonid Chindelevitch, Martin Ester:
Aristotle: stratified causal discovery for omics data. 42 - Elena Rojano, Fernando Moreno Jabato, James Richard Perkins, José Córdoba-Caballero, Federico García-Criado, Ian Sillitoe, Christine A. Orengo, Juan A. G. Ranea, Pedro Seoane-Zonjic:
Assigning protein function from domain-function associations using DomFun. 43 - Vy Nguyen, Johannes Griss:
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, Salil S. Bhate, Graham L. Barlow, Darci Phillips, Wendy J. Fantl, Garry P. Nolan, Christian M. Schürch:
CellSeg: a robust, pre-trained nucleus segmentation and pixel quantification software for highly multiplexed fluorescence images. 46 - Il-Hyung Lee, Sam Passaro, Selin Ozturk, Juan Ureña, Weitian Wang:
Intelligent fluorescence image analysis of giant unilamellar vesicles using convolutional neural network. 48 - Brandon Signal, Tim Kahlke:
how_are_we_stranded_here: quick determination of RNA-Seq strandedness. 49 - Albert Rosenberger, Viola Tozzi, Heike Bickeböller, Rayjean J. Hung, David C. Christiani, Neil E. Caporaso, Geoffrey Liu, Stig E. Bojesen, Loic Le Marchand, Demetrios Albanes, Melinda C. Aldrich, Adonina Tardon, Guillermo Fernández-Tardón, Gad Rennert, John K. Field, Mike Davies, Triantafillos Liloglou, Lambertus A. Kiemeney, Philip Lazarus, Aage Haugen, Shanbeh Zienolddiny, Stephen Lam, Matthew B. Schabath, Angeline S. Andrew, Eric J. Duell, Susanne M. Arnold, Hans Brunnström, Olle Melander, Gary E. Goodman, Chu Chen, Jennifer A. Doherty, Marion Dawn Teare, Angela Cox, Penella J. Woll, Angela Risch, Thomas R. Muley, Mikael Johansson, Paul Brennan, Maria Teresa Landi, Sanjay Shete, Christopher I. Amos:
Iam hiQ - a novel pair of accuracy indices for imputed genotypes. 50 - Zhaonan Zou, Michio Iwata, Yoshihiro Yamanishi, Shinya Oki:
Epigenetic landscape of drug responses revealed through large-scale ChIP-seq data analyses. 51 - Gavin Mackenzie, Rasmus W. Jensen, Thomas Lavstsen, Thomas D. Otto:
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, Drew Ferrell, George V. Popescu:
NetSeekR: a network analysis pipeline for RNA-Seq time series data. 54 - Sonja Mathias, Adrien Coulier, Andreas Hellander:
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, Junior Ocira, Diane Duroux, Ramouna Fouladi, Miha Moskon, Damjana Rozman, Kristel Van Steen:
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, Frida Eiengård, Anna Rohlin, Marcela Dávila López:
PΨFinder: a practical tool for the identification and visualization of novel pseudogenes in DNA sequencing data. 59 - Cinzia Klemm, Rowan S. M. Howell, Peter H. Thorpe:
ScreenGarden: a shinyR application for fast and easy analysis of plate-based high-throughput screens. 60 - Luis Kuhn Cuellar, Andreas Friedrich, Gisela Gabernet, Luis de la Garza, Sven Fillinger, Adrian Seyboldt, Tobias Koch, Sven zur Oven-Krockhaus, Friederike Wanke, Sandra Richter, Wolfgang Maximilian Thaiss, Marius Horger, Nisar Malek, Klaus Harter, Michael Bitzer, Sven Nahnsen:
A data management infrastructure for the integration of imaging and omics data in life sciences. 61 - Walker Gussler, David S. Campo, Zoya Dimitrova, Pavel Skums, Yury Khudyakov:
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, Yi-Fu Weng, Wei-Ting Chang, Fu-An Lin, Giacomo Cavalli:
HiCmapTools: a tool to access HiC contact maps. 64 - Juliane Pfeil, Alina S. Nechyporenko, Marcus Frohme, Frank T. Hufert, Katja Schulze:
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, Giorgio Tumino, Roeland E. Voorrips, Paul Arens, Marinus J. M. Smulders, Eric van de Weg, Chris Maliepaard:
Multiallelic models for QTL mapping in diverse polyploid populations. 67 - Min Xie, Linfeng Yang, Chenglin Jiang, Shenshen Wu, Cheng Luo, Xin Yang, Lijuan He, Shixuan Chen, Tianquan Deng, Mingzhi Ye, Jianbing Yan, Ning Yang:
gcaPDA: a haplotype-resolved diploid assembler. 68 - Ziyin Xin, Yujun Cai, Louis T. Dang, Hannah M. S. Burke, Jerico Revote, Natalie Charitakis, Denis Bienroth, Hieu T. Nim, Yuan-Fang Li, Mirana Ramialison:
MonaGO: a novel gene ontology enrichment analysis visualisation system. 69 - Cheng Peng, Xinben Zhang, Zhijian Xu, Zhaoqiang Chen, Yanqing Yang, Tingting Cai, Weiliang Zhu:
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, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei:
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, Jian-Yu Shi, Wenmin Dong:
Predict multi-type drug-drug interactions in cold start scenario. 75 - Eryk Kropiwnicki, Alexander Lachmann, Daniel J. B. Clarke, Zhuorui Xie, Kathleen M. Jagodnik, Avi Ma'ayan:
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. 76 - Olivér M. Balogh, Bettina Benczik, András Horváth, Mátyás Pétervári, Péter Csermely, Péter Ferdinandy, Bence Ágg:
Efficient link prediction in the protein-protein interaction network using topological information in a generative adversarial network machine learning model. 78 - Jakob P. Pettersen, Eivind Almaas:
csdR, an R package for differential co-expression analysis. 79 - Leonardo R. Souza, Juan Gabriel Colonna, Joseana Macêdo Fechine, Felipe G. Naveca:
Using amino acids co-occurrence matrices and explainability model to investigate patterns in dengue virus proteins. 80 - Modupeore O. Adetunji, Brian J. Abraham:
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. 77 - Jie Hou, Xiufen Ye, Weixing Feng, Qiaosheng Zhang, Yatong Han, Yusong Liu, Yu Li, Yufen Wei:
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, Victor X. Jin, Magnar Bjørås, Junbai Wang:
abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis. 83 - Florin Ratajczak, Mitchell Joblin, Martin Ringsquandl, Marcel Hildebrandt:
Task-driven knowledge graph filtering improves prioritizing drugs for repurposing. 84 - Wiktor Kusmirek, Robert M. Nowak:
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, Tin Nguyen, Duc-Hau Le:
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, Limsoon Wong:
EnsembleFam: towards more accurate protein family prediction in the twilight zone. 90 - Shang Liu, Hailiang Cheng, Javaria Ashraf, Youping Zhang, Qiaolian Wang, Limin Lv, Man He, Guoli Song, Dongyun Zuo:
Interpretation of convolutional neural networks reveals crucial sequence features involving in transcription during fiber development. 91 - Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng:
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. 92 - Yiyu Hong, Juyong Lee, Junsu Ko:
A-Prot: protein structure modeling using MSA transformer. 93 - Francis C. Motta, Robert C. Moseley, Bree Cummins, Anastasia Deckard, Steven B. Haase:
Conservation of dynamic characteristics of transcriptional regulatory elements in periodic biological processes. 94 - Robert Logan, Zoe Fleischmann, Sofia Annis, Amy Wangsness Wehe, Jonathan L. Tilly, Dori C. Woods, Konstantin Khrapko:
3GOLD: optimized Levenshtein distance for clustering third-generation sequencing data. 95 - Michela Quadrini, Sebastian Daberdaku, Carlo Ferrari:
Hierarchical representation for PPI sites prediction. 96 - Michael Lau, Claudia Wigmann, Sara Kress, Tamara Schikowski, Holger Schwender:
Evaluation of tree-based statistical learning methods for constructing genetic risk scores. 97 - Malcolm E. Fisher, Erik Segerdell, Nicolas Matentzoglu, Mardi J. Nenni, Joshua D. Fortriede, Stanley Chu, Troy J. Pells, David Osumi-Sutherland, Praneet Chaturvedi, Christina James-Zorn, Nivitha Sundararaj, Vaneet S. Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov, Bradley I. Arshinoff, Kamran Karimi, Peter D. Vize, Aaron M. Zorn:
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development. 99 - Katarzyna Stapor, Krzysztof Kotowski, Tomasz Smolarczyk, Irena Roterman:
Lightweight ProteinUnet2 network for protein secondary structure prediction: a step towards proper evaluation. 100 - Lindsay V. Clark, Wittney Mays, Alexander E. Lipka, Erik J. Sacks:
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, Hyunwoo J. Kim, Daniel J. Garry, Il-Youp Kwak:
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, Julian Reading, Lucas T. Graybuck, Peter J. Skene:
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, Eunok Paek:
TIDD: tool-independent and data-dependent machine learning for peptide identification. 109 - Josip Rudar, Teresita M. Porter, Michael Wright, Geoffrey Brian Golding, Mehrdad Hajibabaei:
LANDMark: an ensemble approach to the supervised selection of biomarkers in high-throughput sequencing data. 110 - Stefano Marchesin, Gianmaria Silvello:
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, Pedro de los Reyes, Mercedes García-González, Francisco José Romero-Campero:
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, Mark Wappett, Bruce Seligmann, Daniel B. Longley, Simon S. McDade:
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, Azat K. Garaev, Alexander V. Tyakht, Sergey V. Ulianov, Sergey V. Razin:
Pentad: a tool for distance-dependent analysis of Hi-C interactions within and between chromatin compartments. 116 - Borja González-Seoane, Christian Ponte-Fernández, Jorge González-Domínguez, María J. Martín:
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models. 117 - Raul I. Perez Martell, Alison Ziesel, Hosna Jabbari, Ulrike Stege:
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, Lazaros G. Papageorgiou, Sophia Tsoka:
Novel drug-target interactions via link prediction and network embedding. 121 - Don Neumann, Anireddy S. N. Reddy, Asa Ben-Hur:
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. 142 - Forough Firoozbakht, Iman Rezaeian, Luis Rueda, Alioune Ngom:
Computationally repurposing drugs for breast cancer subtypes using a network-based approach. 143 - Usman Naseem, Adam G. Dunn, Matloob Khushi, Jinman Kim:
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, Ana C. Marques, Sven Bergmann:
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. 147 - Alessia Auriemma Citarella, Luigi Di Biasi, Michele Risi, Genoveffa Tortora:
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, Marco J. Morelli, Marco Masseroli:
Accurate and highly interpretable prediction of gene expression from histone modifications. 151 - Meiling Liu, Juna Goo, Yang Liu, Wei Sun, Michael C. Wu, Li Hsu, Qianchuan He:
TCR-L: an analysis tool for evaluating the association between the T-cell receptor repertoire and clinical phenotypes. 152 - Jin-Ok Lee, Jiyon Chu, Gyuyeon Jang, Minho Lee, Yeun-Jun Chung:
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, Stephen P. Ficklin:
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, Sukki Cho, Jin-Haeng Chung, Han-Kwang Yang, Jong-Il Kim:
Expression-based species deconvolution and realignment removes misalignment error in multispecies single-cell data. 157 - Mateo Gray, Sean Chester, Hosna Jabbari:
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, Trees-Juen Chuang:
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, Giulia Fiscon:
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, Caterina M. Scoglio:
A global $Anopheles\ gambiae$ gene co-expression network constructed from hundreds of experimental conditions with missing values. 170 - Gustavo Sganzerla Martinez, Ernesto Pérez-Rueda, Sharmilee Sarkar, Aditya Kumar, Scheila de Avila e Silva:
Machine learning and statistics shape a novel path in archaeal promoter annotation. 171 - Nikola Benes, Lubos Brim, Jakub Kadlecaj, Samuel Pastva, David Safránek:
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, Arokiaraj Sherlin Rosita, Medha Pandya, Jayaraman Selvaraj, Lokesh Ravi, Nalini Devarajan, Mukesh Doble:
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, Xiuru Dai, Daohong Fu, Pinghua Li, Baijuan Du:
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, Mayte Suárez-Fariñas:
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, Zhaleh Safikhani, Wail Ba-alawi, Farnoosh Khodakarami, Eva Lin, Yihong Yu, Scott Martin, Janosch Ortmann, Tero Aittokallio, Marc Hafner, Benjamin Haibe-Kains:
Evaluation of statistical approaches for association testing in noisy drug screening data. 188 - Ying Liang, Ze-Qun Zhang, Nian-Nian Liu, Ya-Nan Wu, Chang-Long Gu, Ying-Long Wang:
MAGCNSE: predicting lncRNA-disease associations using multi-view attention graph convolutional network and stacking ensemble model. 189 - Federica Conte, Federico Papa, Paola Paci, Lorenzo Farina:
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, Helena Aidos, Sara C. Madeira:
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, Zhe-Xiong Lian, Zhi Liang, Jia-Rui Wu:
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, Phuoc Thien Truong Nguyen, Tarja Sironen, Olli Vapalahti, Teemu Smura, Ravi Kant:
ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies. 196 - Jayadev Joshi, Daniel J. Blankenberg:
PDAUG: a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling. 197 - Felix Van der Jeugt, Peter Dawyndt, Bart Mesuere:
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, Renato Arroyo-Duarte, Fernando Rincón-Vieyra, Matías Alvarado-Mentado:
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, Kang-Hsin Wang, Yi-Hau Chen:
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, Lucia Sanchez-Gonzalez, Ricardo Ramos-Ruiz, Luis del Peso:
Hypoxia classifier for transcriptome datasets. 204 - Edwin S. Dalmaijer, Camilla L. Nord, Duncan E. Astle:
Statistical power for cluster analysis. 205 - Pablo Flores, Miquel Salicru, Alex Sánchez-Pla, Jordi Ocaña:
An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment. 207 - Zachary R. McCaw, Hugues Aschard, Hanna Julienne:
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, Fenia Christopoulou, Meizhi Ju, Makoto Miwa, Sophia Ananiadou:
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, Xiaofei Qin, Lele Liu, Xuedian Zhang:
Multi-type feature fusion based on graph neural network for drug-drug interaction prediction. 224 - Matthis Ebel, Giovanna Migliorelli, Mario Stanke:
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, Julian Cascitti, Bertil Schmidt:
CARE 2.0: reducing false-positive sequencing error corrections using machine learning. 227 - Verena E. Kutschera, Marcin Kierczak, Tom van der Valk, Johanna von Seth, Nicolas Dussex, Edana Lord, Marianne Dehasque, David W. G. Stanton, Payam Emami Khoonsari, Björn Nystedt, Love Dalén, David Díez-del-Molino:
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species. 228 - Steven Gore, Rajeev K. Azad:
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, Katherine W. Klinger, Deepak K. Rajpal, Cheng Zhu, Erin Teeple:
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, Vahid Shahrezaei, Marc Sturrock:
Benchmarking imputation methods for network inference using a novel method of synthetic scRNA-seq data generation. 236 - Nelson R. C. Monteiro, Carlos J. V. Simões, Henrique V. Ávila, Maryam Abbasi, José Luís Oliveira, Joel P. Arrais:
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, Christina Larsson, Magnus Simonsson, Patrik Ellström:
rprimer: an R/bioconductor package for design of degenerate oligos for sequence variable viruses. 239 - H. Busra Cagirici, Hikmet Budak, Taner Z. Sen:
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, Markus Vähä-Koskela, Jing Tang, ZiaurRehman Tanoli:
Using BERT to identify drug-target interactions from whole PubMed. 245 - Vladimir Nikolic, Amirhossein Afshinfard, Justin Chu, Johnathan Wong, Lauren Coombe, Ka Ming Nip, René L. Warren, Inanç Birol:
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, Qurat ul Ain Farooq, Shanshan Tu, Chuangbai Xiao, Saqib Ali:
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, M. Ciullo, FranceGenRef Consortium, Anne-Louise Leutenegger, H. Perdry:
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, Yanan Wu, Ze-Qun Zhang, Nian-Nian Liu, Jun Peng, Jianjun Tang:
Hyb4mC: a hybrid DNA2vec-based model for DNA N4-methylcytosine sites prediction. 258 - Jinghang Gu, Rong Xiang, Xing Wang, Jing Li, Wenjie Li, Longhua Qian, Guodong Zhou, Chu-Ren Huang:
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, Carlos Guerrero-Bosagna, John B. O. Mitchell, Per Jensen, V. Anne Smith:
Practical application of a Bayesian network approach to poultry epigenetics and stress. 261 - Blaise Hanczar, Victoria Bourgeais, Farida Zehraoui:
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, Silpa ChandraBhasi Sindhu, Sa'ed Abed:
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, Tim W. Nattkemper, Karsten Niehaus, Stefan P. Albaum:
MetHoS: a platform for large-scale processing, storage and analysis of metabolomics data. 267 - Vincent Moco, Damien Cazenave, Maëlle Garnier, Matthieu Pot, Isabel Marcelino, Antoine Talarmin, Stéphanie Guyomard-Rabenirina, Sébastien Breurec, Séverine Ferdinand, Alexis Dereeper, Yann Reynaud, David Couvin:
getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories. 268 - Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi:
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, Xiaowo Wang:
Correction to: DeSP: a systematic DNA storage error simulation pipeline. 274 - Junaid Rashid, Jungeun Kim, Amir Hussain, Usman Naseem, Sapna Juneja:
A novel multiple kernel fuzzy topic modeling technique for biomedical data. 275 - Ronghui Li, Bella Banjanin, Rebekka K. Schneider, Ivan G. Costa:
Detection of cell markers from single cell RNA-seq with sc2marker. 276 - Chenye Wang, Junhan Shi, Jiansheng Cai, Yusen Zhang, Xiaoqi Zheng, Naiqian Zhang:
DriverRWH: discovering cancer driver genes by random walk on a gene mutation hypergraph. 277 - Reza Hassanzadeh, Soheila Shabani-Mashcool:
Does adding the drug-drug similarity to drug-target interaction prediction methods make a noticeable improvement in their efficiency? 278 - Maximilian Sprang, Miguel A. Andrade-Navarro, Jean-Fred Fontaine:
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, Xi Zhang, Yuying Zhou, Ying Han, Qing Wang:
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, Jian Liu, Jianlin Cheng:
Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps. 283 - Huiping Shi, Liang Gao, Weili Zhang, Min Jiang:
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, Jacob Durtschi, Ana Kellogg, Tracey Lewis, Devin Close, Hunter Best:
Algorithmic improvements for discovery of germline copy number variants in next-generation sequencing data. 285 - Daniel Flatschacher, Verena Speckbacher, Susanne Zeilinger:
qRAT: an R-based stand-alone application for relative expression analysis of RT-qPCR data. 286 - Konstantin Bob, David Teschner, Thomas Kemmer, David Gomez-Zepeda, Stefan Tenzer, Bertil Schmidt, Andreas Hildebrandt:
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, Eman A. Al-Hada, Shamsan A. Al-Murisi, Ahmed A. Al-kuhali, Ammar A. Q. Aldaifl, Mohammed Elmustafa Amin:
Multiview clustering of multi-omics data integration by using a penalty model. 288 - Tuomas Kaseva, Bahareh Omidali, Eero Hippeläinen, Teemu Mäkelä, Ulla Wilppu, Alexey Sofiev, Arto Merivaara, Marjo Yliperttula, Sauli Savolainen, Eero Salli:
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, Mehmet M. Dalkilic:
ccImpute: an accurate and scalable consensus clustering based algorithm to impute dropout events in the single-cell RNA-seq data. 291 - Stefan Röder, Gunda Herberth, Ana C. Zenclussen, Mario Bauer:
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses. 292 - Ozan Ozisik, Morgane Térézol, Anaïs Baudot:
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. 293 - Hansen Chen, Jianhua Chen, Zhiwen Lu, Rongshu Wang:
CMIC: an efficient quality score compressor with random access functionality. 294 - Alessio Mascolini, Dario Cardamone, Francesco Ponzio, Santa Di Cataldo, Elisa Ficarra:
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, Lei Liu:
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, Amirreza Kazemi, Kimia Hamidieh, Hamed Dashti, Maedeh-sadat Tahaei, Hamid R. Rabiee, Hamid Alinejad-Rokny, Iman Dehzangi:
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, Moshe Carroll, S. Lazarev, J. Eduardo Fajardo, András Fiser, Raji Viswanathan:
Integrated structure-based protein interface prediction. 301 - Katherine James, Aoesha Alsobhe, Simon J. Cockell, Anil Wipat, Matthew R. Pocock:
Integration of probabilistic functional networks without an external Gold Standard. 302 - Weidong Xie, Wei Li, Shoujia Zhang, Linjie Wang, Jinzhu Yang, Dazhe Zhao:
A novel biomarker selection method combining graph neural network and gene relationships applied to microarray data. 303 - Adam N. Bennett, Jethro Rainford, Xiaotai Huang, Qian He, Kei Hang Katie Chan:
Canary: an automated tool for the conversion of MaCH imputed dosage files to PLINK files. 304 - Ronald de Vlaming, Eric A. W. Slob, Patrick J. F. Groenen, Cornelius A. Rietveld:
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, Jakob Zierk, Manfred Rauh, Markus Metzler, Sarem Seitz:
Mixture density networks for the indirect estimation of reference intervals. 307 - Xinyu He, Ping Tai, Hongbin Lu, Xin Huang, Yonggong Ren:
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, Mahmoud Rafieian-Kopaei, Korosh Ashrafi Dehkordi, Hamidreza Pazoki-Toroudi, Fatemeh Azadegan-Dehkordi, Gholam-Reza Mobini, Morteza Alizadeh, Muhammad Sadeqi Nezhad, Maryam Ghasemi-Dehnoo, Nader Bagheri:
In silico design of a multi-epitope vaccine against HPV16/18. 311 - Jiacheng Wu, Ni Li, Linwen Zhu, Dawei Zhen, Mengqi Li, Hang Chen, Mengmeng Ye, Yiqin Wei, Guofeng Shao:
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, Martin Dugas:
Cogito: automated and generic comparison of annotated genomic intervals. 315 - Kolja Thormann, Viola Tozzi, Paul Stärke, Heike Bickeböller, Marcus Baum, Albert Rosenberger:
ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures. 316 - Sierra S. Nishizaki, Alan P. Boyle:
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, Shubham Vashishtha, Bishwajit Kundu, Monidipa Ghosh:
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, Ru Wang, Qing Yu, Catherine J. Huntoon, Larry M. Karnitz, Scott H. Kaufmann, Steven P. Gygi, Michael J. Birrer, Amanda G. Paulovich, Jie Peng, Pei Wang:
DAGBagM: learning directed acyclic graphs of mixed variables with an application to identify protein biomarkers for treatment response in ovarian cancer. 321 - Yawu Zhao, Shudong Wang, Yande Ren, Yulin Zhang:
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, María Ortiz, Jon Pey:
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, Pingzhao Hu:
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, Rasmus Nielsen:
SCONCE2: jointly inferring single cell copy number profiles and tumor evolutionary distances. 348 - Niraj Thapa, Meenal Chaudhari, Sean McManus, Kaushik Roy, Robert H. Newman, Hiroto Saigo, K. C. Dukka B.:
Correction: DeepSuccinylSite: a deep learning based approach for protein succinylation site prediction. 349 - Linrong Li, Lin Li, Qiang Sun:
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, Yili Wang, Zhen Liu, Yuanning Liu:
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, Miran Kim, Xiaoqian Jiang, Arif Ozgun Harmanci:
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, Vikram Sunkara, Sagar Khavnekar, Florian Beck, Robert Brandt, Daniel Baum:
Volumetric macromolecule identification in cryo-electron tomograms using capsule networks. 360 - David Chardin, Cyprien Gille, Thierry Pourcher, Olivier Humbert, Michel Barlaud:
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, Angela Wei, Valerie A. Arboleda:
DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features. 364 - Fanny Mollandin, Hélène Gilbert, Pascal Croiseau, Andrea Rau:
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, Keqiao Li, Menghan Lin, Feng Pan, Wei Wu, Jinfeng Zhang:
A reinforcement learning approach for protein-ligand binding pose prediction. 368 - Mohammad Taheri-Ledari, Amirali Zandieh, Seyed Peyman Shariatpanahi, Changiz Eslahchi:
Assignment of structural domains in proteins using diffusion kernels on graphs. 369 - Mayank Baranwal, Abram Magner, Jacob Saldinger, Emine Sumeyra Turali-Emre, Paolo Elvati, Shivani Kozarekar, J. Scott Vanepps, Nicholas A. Kotov, Angela Violi, Alfred O. Hero III:
Struct2Graph: a graph attention network for structure based predictions of protein-protein interactions. 370 - Osamu Maruyama, Yinuo Li, Hiroki Narita, Hidehiro Toh, Wan Kin Au Yeung, Hiroyuki Sasaki:
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, Nan Xu, Chengkui Zhao, Jiayu Xu, Liqing Kang, Xiaoyan Lou, Lei Yu, Weixing Feng:
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, Avi Ma'ayan:
Transforming L1000 profiles to RNA-seq-like profiles with deep learning. 374 - Juan O. Lopez, Jaime Seguel, Andres Chamorro, Kenneth S. Ramos:
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, Julia Brunmair, Christoph Bueschl, Christopher Gerner, Jürgen Zanghellini:
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, Junyi Tong, Xiangling Fu:
Topology-enhanced molecular graph representation for anti-breast cancer drug selection. 382 - Heesun Kim, Mikang Sim, Na Young Park, Kisang Kwon, Junyoung Kim, Jaebum Kim:
msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. 383 - Dmitry Evgenevich Mylarshchikov, Andrey Alexandrovich Mironov:
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, Matthew England:
Polynomial superlevel set representation of the multistationarity region of chemical reaction networks. 391 - Petr Rysavý, Jirí Kléma, Michaela Dostálová Merkerová:
circGPA: circRNA functional annotation based on probability-generating functions. 392 - Bilin Liang, Haifan Gong, Lu Lu, Jie Xu:
Risk stratification and pathway analysis based on graph neural network and interpretable algorithm. 394 - Sonja Zehetmayer, Martin Posch, Alexandra Graf:
Impact of adaptive filtering on power and false discovery rate in RNA-seq experiments. 388 - E. C. Wood, Amy Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki, Stephen A. Ramsey:
RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. 400 - Tommaso Alfonsi, Anna Bernasconi, Arif Canakoglu, Marco Masseroli:
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, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng, Yi-Yan Lei:
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, Xiaoqian Jiang, Arif Ozgun Harmanci:
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, Junfen Lin, Ke Lyu, Zexu Wu, Yuhao Chen, Yinwei Qiu, Yanrong Zhao, Wei Wang, Tianxiang Lin, Huiyun Pan, Ming Chen:
A machine learning-based data mining in medical examination data: a biological features-based biological age prediction model. 411 - Yingxia Li, Ulrich Mansmann, Shangming Du, Roman Hornung:
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, Huimin Ma:
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, Jamie Gorzynski, Gonzalo Yebra, Tim Angus, J. Ross Fitzgerald, Tom C. Freeman:
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, Zhuowei Gao, Yongle Ju:
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, Wei-Ting Hwang:
Estimating the effect size of a hidden causal factor between SNPs and a continuous trait: a mediation model approach. 420 - Camille Clouard, Kristiina Ausmees, Carl Nettelblad:
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, Aurélie Pirayre, Frédérique Bidard, Laurent Duval, Fragkiskos D. Malliaros:
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, Jonathon Lillia, Ashnil Kumar, Paula Bray, Jinman Kim, Joshua Burns, Tegan L. Cheng:
Clinical applications of machine learning in predicting 3D shapes of the human body: a systematic review. 431 - Ruiyu Guo, Hailin Chen, Wengang Wang, Guangsheng Wu, Fangliang Lv:
Predicting potential miRNA-disease associations based on more reliable negative sample selection. 432 - Yang Yang, Zhouyao Qian, Mingyang Feng, Weiting Liao, Qiuji Wu, Feng Wen, Qiu Li:
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, Thomas F. Meyer, André P. Mäurer:
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, Giorgio Tumino:
PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. 442 - Mykyta Matushyn, Madhuchanda Bose, Abdallah Amr Mahmoud, Lewis Cuthbertson, Carlos Tello, Karatug Ozan Bircan, Andrew Terpolovsky, Varuna Bamunusinghe, Umar Khan, Biljana Novkovic, Manfred G. Grabherr, Puya G. Yazdi:
SumStatsRehab: an efficient algorithm for GWAS summary statistics assessment and restoration. 443 - Lin Zhu, Xiaoyu Wang, Fuyi Li, Jiangning Song:
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, Martin Figeac, Sandrine Geffroy, Maxime Bucci, Karine Celli-Lebras, Matthieu Duchmann, Romane Joudinaud, Laurène Fenwarth, Olivier Nibourel, Laure Goursaud, Raphael Itzykson, Hervé Dombret, Mathilde Hunault, Claude Preudhomme, Mikaël Salson:
Frugal alignment-free identification of FLT3-internal tandem duplications with FiLT3r. 448 - Corey Weistuch, Jiening Zhu, Joseph O. Deasy, Allen R. Tannenbaum:
The maximum entropy principle for compositional data. 449 - Jianhua Jia, Genqiang Wu, Meifang Li, Wangren Qiu:
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, Jiazheng Liu, Lijun Shen, Xi Chen, Qiwei Xie, Hua Han:
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, Aoi Hatae, Yukie Sakai, Fred C. Boogerd, Hiroyuki Kurata:
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, Jennifer L. Wilding, Walter F. Bodmer:
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, Chen Cao:
A novel method for drug-target interaction prediction based on graph transformers model. 459 - Hui Li, Davis J. McCarthy, Heejung Shim, Susan Wei:
Trade-off between conservation of biological variation and batch effect removal in deep generative modeling for single-cell transcriptomics. 460 - Sylwan Rahardja, Mou Wang, Binh P. Nguyen, Pasi Fränti, Susanto Rahardja:
A lightweight classification of adaptor proteins using transformer networks. 461 - Nathan P. Gill, Raji Balasubramanian, James R. Bain, Michael J. Muehlbauer, William L. Lowe, Denise M. Scholtens:
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, Marco Martínez-Sánchez, Juan Touriño:
SparkEC: speeding up alignment-based DNA error correction tools. 464 - Yekai Zhou, Amy Wing-Sze Leung, Syed Shakeel Ahmed, Tak Wah Lam, Ruibang Luo:
Duet: SNP-assisted structural variant calling and phasing using Oxford nanopore sequencing. 465 - Emmanuel Onah, Philip F. Uzor, Ikenna Calvin Ugwoke, Jude Uche Eze, Sunday Tochukwu Ugwuanyi, Ifeanyi Richard Chukwudi, Akachukwu Ibezim:
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, Yi-Hui Zhou:
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, Rachel P. J. Lai, Timothy M. D. Ebbels:
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 - Eunbyul 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, Sanne Abeln, Juan J. Garcia-Vallejo:
INFLECT: an R-package for cytometry cluster evaluation using marker modality. 487 - Igor V. Deyneko, Orkhan N. Mustafaev, Alexander Tyurin, Ksenya V. Zhukova, Alexander Varzari, Irina V. Goldenkova-Pavlova:
Modeling and cleaning RNA-seq data significantly improve detection of differentially expressed genes. 488 - Brian Vestal, Elizabeth Wynn, Camille M. Moore:
lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models. 489 - Thomas J. Nicholas, Michael J. Cormier, Aaron R. Quinlan:
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, Chandrashekar Karunakaran, Jyoti Shetty, Jitendra Kumar, Vidya Niranjan:
Implementation of ensemble machine learning algorithms on exome datasets for predicting early diagnosis of cancers. 496 - Xuewen Wang, Bruce Budowle, Jianye Ge:
USAT: a bioinformatic toolkit to facilitate interpretation and comparative visualization of tandem repeat sequences. 497 - Jean-Tristan Brandenburg, Lindsay Clark, Gerrit Botha, Sumir Panji, Shakuntala Baichoo, Christopher J. Fields, Scott Hazelhurst:
H3AGWAS: a portable workflow for genome wide association studies. 498 - Adrien Vidal, Franck Gauthier, Willy Rodrigez, Nadège Guiglielmoni, Damien Leroux, Nicolas Chevrolier, Sylvain Jasson, Elise Tourrette, Olivier C. Martin, Matthieu Falque:
SeSAM: software for automatic construction of order-robust linkage maps. 499 - Akio Miyao, Utako Yamanouchi:
Transposable element finder (TEF): finding active transposable elements from next generation sequencing data. 500 - Xiangwen Zheng, Haijian Du, Xiaowei Luo, Fan Tong, Wei Song, Dongsheng Zhao:
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, Na Han, Yexiao Cheng, Jingzhe Shang, Shenghui Weng, Rong Yang, Hangyu Zhou, Aiping Wu:
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, David A. Liberles:
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, Aditya S. Malwe, Gopal N. Srivastava, Parikshit Thoudam, Keshav Hibare, Vineet K. Sharma:
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, Carlos Espinosa-Soto:
Early effects of gene duplication on the robustness and phenotypic variability of gene regulatory networks. 509 - Veronica Gheorghe, Traver Hart:
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, Manish Kumar, Karsten Zengler, Rafael Silva-Rocha, Ricardo Roberto da Silva:
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, Yue Li, Zhong Wang:
Persistent memory as an effective alternative to random access memory in metagenome assembly. 513 - Marta Moreno, Ricardo Vilaça, Pedro G. Ferreira:
Scalable transcriptomics analysis with Dask: applications in data science and machine learning. 514 - Minsoo Kim, Eunjung 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, Luigi Di Biasi, Fabiola De Marco, Genoveffa Tortora:
ENTAIL: yEt aNoTher amyloid fIbrils cLassifier. 517 - Miquel Anglada-Girotto, Samuel Miravet-Verde, Luis Serrano, Sarah A. Head:
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, Ville Mustonen:
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, Hoang Duc Nguyen:
Extract antibody and antigen names from biomedical literature. 524 - Wei Jiang, Xiangyu Zhang, Siting Li, Shuang Song, Hongyu Zhao:
An unbiased kinship estimation method for genetic data analysis. 525 - Sen Wang, Hengchao Wang, Fan Jiang, Anqi Wang, Hangwei Liu, Hanbo Zhao, Boyuan Yang, Dong Xu, Yan Zhang, Wei Fan:
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, Dominic A. Helmerich, Dominik Boras, Markus Sauer, Philip Kollmannsberger:
ReCSAI: recursive compressed sensing artificial intelligence for confocal lifetime localization microscopy. 530 - Felix Nikolaus Wirth, Tobias Kussel, Armin Müller, Kay Hamacher, Fabian Prasser:
EasySMPC: a simple but powerful no-code tool for practical secure multiparty computation. 531 - Augustin Boudry, Sasha Darmon, Nicolas Duployez, Martin Figeac, Sandrine Geffroy, Maxime Bucci, Karine Celli-Lebras, Matthieu Duchmann, Romane Joudinaud, Laurène Fenwarth, Olivier Nibourel, Laure Goursaud, Raphael Itzykson, Hervé Dombret, Mathilde Hunault, Claude Preudhomme, Mikaël Salson:
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, Martin Hemberg:
SC3s: efficient scaling of single cell consensus clustering to millions of cells. 536 - Jero Mario Schäfer, Ming Tang, Danny Luu, Anke Bergmann, Lena Wiese:
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, Kenny H. Cha, Nicholas Petrick, Mike Mikailov:
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, Laszlo Szekely, Ingemar Ernberg, Andrii Savchenko:
AtlasGrabber: a software facilitating the high throughput analysis of the human protein atlas online database. 546 - Alejandro Cisterna, Aurora González-Vidal, Daniel Ruiz, Jordi Ortiz, Alicia Gómez-Pascual, Zhongbo Chen, Mike A. Nalls, Faraz Faghri, John Hardy, Irene Díez, Paolo Maietta, Sara Álvarez, Mina Ryten, Juan A. Botía:
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, Marco Masseroli:
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, Vincen Wu, Matthew R. Lewis, Zoltan Takats:
Mass recalibration for desorption electrospray ionization mass spectrometry imaging using endogenous reference ions. 133 - Emanuele Marchi, Mathew Jones, Paul Klenerman, John Frater, Gkikas Magiorkinis, Robert Belshaw:
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, Jianing Zhao, Siyu Han, Yu Zhang, Wei Du:
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, Wouter Deelder, Daniel Ward, Susana G. Campino, Martin L. Hibberd, Taane G. Clark:
COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data. 137 - Hamed Dashti, Iman Dehzangi, Masroor Bayati, James Breen, Amin Beheshti, Nigel H. Lovell, Hamid R. Rabiee, Hamid Alinejad-Rokny:
Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. 138 - Sebastian Winkler, Ivana Winkler, Mirjam Figaschewski, Thorsten Tiede, Alfred Nordheim, Oliver Kohlbacher:
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. 139 - Anni A. Antikainen, Markus Heinonen, Harri Lähdesmäki:
Modeling binding specificities of transcription factor pairs with random forests. 212 - Tiantian Liu, Chao Zhou, Huimin Wang, Hongyu Zhao, Tao Wang:
phyloMDA: an R package for phylogeny-aware microbiome data analysis. 213 - Sebastian Raubach, Miriam Schreiber, Paul D. Shaw:
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, Geoffrey Thomson, Emilie Péry, Frédéric Chausse, Christophe Tatout, Sophie Desset, Josien C. van Wolfswinkel, Yannick Jacob:
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, Matteo Smerlak:
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, David Gfeller:
Metacells untangle large and complex single-cell transcriptome networks. 336 - Xingang Jia, Qiuhong Han, Zuhong Lu:
Constructing the boundary between potent and ineffective siRNAs by MG-algorithm with C-features. 337 - Susanna R. Grigson, Jody C. McKerral, James G. Mitchell, Robert A. Edwards:
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, Dongsheng Wang, Huaichao Luo:
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, Hongmei Zhang, Fugen Gao:
Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression. 434 - Zezhou Hao, Pengchen Liang, Changyu He, Shuang Sha, Ziyuan Yang, Yixin Liu, Junfeng Shi, Zhenggang Zhu, Qing Chang:
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, Tieliang Gong, Erik Cambria, Chen Li:
JCBIE: a joint continual learning neural network for biomedical information extraction. 549 - Dustin Kenefake, Erick Armingol, Nathan E. Lewis, Efstratios N. Pistikopoulos:
An improved algorithm for flux variability analysis. 550 - Askar Gafurov, Andrej Baláz, Fabian Amman, Kristína Borsová, Viktória Cabanová, Boris Klempa, Andreas Bergthaler, Tomás Vinar, Brona Brejová:
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, Sarbajeet Tiwari:
Symptoms are known by their companies: towards association guided disease diagnosis assistant. 556 - Xuedong Wang, Yanle Liu, Xinyao Miao, Yin Chen, Xiao Cao, Yuchen Zhang, Shuaicheng Li, Qin Zhou:
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, Santiago Cuesta-López, César Ignacio García-Osorio, Javier Pérez-Rodríguez, Nicolás García-Pedrajas:
Nonlinear physics opens a new paradigm for accurate transcription start site prediction. 565 - Max van 't Hof, Omkar S. Mohite, Jonathan M. Monk, Tilmann Weber, Bernhard O. Palsson, Morten O. A. Sommer:
High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917. 566 - Abdullah Soydan Mahmutoglu, Fatma Zeynep Arslan, Mehmet Karagülle, Mehmet Semih Çakir, Özdes 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, Haohui Zhu:
Weakly supervised video-based cardiac detection for hypertensive cardiomyopathy. 163 - Sang Won Jo, Eun Soo Kim, Dae Young Yoon, Mi Jung Kwon:
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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