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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