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New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 2
 
February 2024
 
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Bioframe: operations on genomic intervals in Pandas dataframes border=  
 
Nezar Abdennur, Geoffrey Fudenberg, Ilya M Flyamer, Aleksandra A Galitsyna, Anton Goloborodko ...
 
 
 
Original Papers
 
 
 
 
Genome analysis
 
 
 
 
BCFtools/liftover: an accurate and comprehensive tool to convert genetic variants across genome assemblies border= 
 
Giulio Genovese, Nicole B Rockweiler, Bryan R Gorman, Tim B Bigdeli, Michelle T Pato ...
 
 
 
Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice border= 
 
Bjarne Daenekas, Eilís Pérez, Fabio Boniolo, Sabina Stefan, Salvatore Benfatto ...
 
 
 
Zero is not absence: censoring-based differential abundance analysis for microbiome data border= 
 
Lap Sum Chan, Gen Li
 
 
 
Sequence analysis
 
 
 
 
A simple refined DNA minimizer operator enables 2-fold faster computation border= 
 
Chenxu Pan, Knut Reinert
 
 
 
 
cloudrnaSP Ades: isoform assembly using bulk barcoded RNA sequencing data border= 
 
Dmitry Meleshko, Andrey D Prjbelski, Mikhail Raiko, Alexandru I Tomescu, Hagen Tilgner ...
 
 
 
Using explainable machine learning to uncover the kinase'substrate interaction landscape border= 
 
Zhongliang Zhou, Wayland Yeung, Saber Soleymani, Nathan Gravel, Mariah Salcedo ...
 
 
 
YACHT : an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample border= 
 
David Koslicki, Stephen White, Chunyu Ma, Alexei Novikov
 
 
 
PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction border= 
 
Kexin Shi, Yuanpeng Xiong, Yu Wang, Yifan Deng, Wenjia Wang ...
 
 
 
Protein language models meet reduced amino acid alphabets border=  
 
Ioan Ieremie, Rob M Ewing, Mahesan Niranjan
 
 
 
 
NanoCon: contrastive learning-based deep hybrid network for nanopore methylation detection border= 
 
Chenglin Yin, Ruheng Wang, Jianbo Qiao, Hua Shi, Hongliang Duan ...
 
 
 
DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning border= 
 
Jun Wang, Marc Horlacher, Lixin Cheng, Ole Winther
 
 
 
Highly efficient clustering of long-read transcriptomic data with GeLuster border=  
 
Junchi Ma, Xiaoyu Zhao, Enfeng Qi, Renmin Han, Ting Yu ...
 
 
 
mBARq: a versatile and user-friendly framework for the analysis of DNA barcodes from transposon insertion libraries, knockout mutants, and isogenic strain populations border= 
 
Anna Sintsova, Hans-Joachim Ruscheweyh, Christopher M Field, Lilith Feer, Bidong D Nguyen ...
 
 
 
T-S2Inet: Transformer-based sequence-to-image network for accurate nanopore sequence recognition border= 
 
Xiaoyu Guan, Wei Shao, Daoqiang Zhang
 
 
 
StructuralDPPIV: a novel deep learning model based on atom structure for predicting dipeptidyl peptidase-IV inhibitory peptides border= 
 
Ding Wang, Junru Jin, Zhongshen Li, Yu Wang, Mushuang Fan ...
 
 
 
Phylogenetics
 
 
 
 
Many-core algorithms for high-dimensional gradients on phylogenetic trees border= 
 
Karthik Gangavarapu, Xiang Ji, Guy Baele, Mathieu Fourment, Philippe Lemey ...
 
 
 
Statistical framework to determine indel-length distribution border=  
 
Elya Wygoda, Gil Loewenthal, Asher Moshe, Michael Alburquerque, Itay Mayrose ...
 
 
 
Structural bioinformatics
 
 
 
 
Concurrent prediction of RNA secondary structures with pseudoknots and local 3D motifs in an integer programming framework border= 
 
Gabriel Loyer, Vladimir Reinharz
 
 
 
Multi-indicator comparative evaluation for deep learning-based protein sequence design methods border= 
 
Jinyu Yu, Junxi Mu, Ting Wei, Hai-Feng Chen
 
 
 
PERFUMES: pipeline to extract RNA functional motifs and exposed structures border=  
 
Arnaud Chol, Roman Sarrazin-Gendron, Éric Lécuyer, Mathieu Blanchette, Jérôme Waldispühl
 
 
 
PMIpred: a physics-informed web server for quantitative protein'membrane interaction prediction border= 
 
Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius ...
 
 
 
RNA threading with secondary structure and sequence profile border=  
 
Zongyang Du, Zhenling Peng, Jianyi Yang
 
 
 
Dynamic correlations: exact and approximate methods for mutual information border=  
 
Kemal DemirtaÅŸ, Burak Erman, Türkan HaliloÄŸlu
 
 
 
Geometry-complete perceptron networks for 3D molecular graphs border=  
 
Alex Morehead, Jianlin Cheng
 
 
 
Gene expression
 
 
 
 
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data border= 
 
Mikaela Koutrouli, Katerina Nastou, Pau Piera Líndez, Robbin Bouwmeester, Simon Rasmussen ...
 
 
 
DESpace : spatially variable gene detection via differential expression testing of spatial clusters border= 
 
Peiying Cai, Mark D Robinson, Simone Tiberi
 
 
 
scCancer2: data-driven in-depth annotations of the tumor microenvironment at single-level resolution border= 
 
Zeyu Chen, Yuxin Miao, Zhiyuan Tan, Qifan Hu, Yanhong Wu ...
 
 
 
scKWARN: Kernel-weighted-average robust normalization for single-cell RNA-seq data border= 
 
Chih-Yuan Hsu, Chia-Jung Chang, Qi Liu, Yu Shyr
 
 
 
Deep centroid: a general deep cascade classifier for biomedical omics data classification border= 
 
Kuan Xie, Yuying Hou, Xionghui Zhou
 
 
 
CTISL: a dynamic stacking multi-class classification approach for identifying cell types from single-cell RNA-seq data border= 
 
Xiao Wang, Ziyi Chai, Shaohua Li, Yan Liu, Chen Li ...
 
 
 
AGImpute: imputation of scRNA-seq data based on a hybrid GAN with dropouts identification border= 
 
Xiaoshu Zhu, Shuang Meng, Gaoshi Li, Jianxin Wang, Xiaoqing Peng
 
 
 
Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data border= 
 
Juanru Guo, Wenjin Zhang, Xuhua Chen, Allen Yen, Lucy Chen ...
 
 
 
Phenotype prediction from single-cell RNA-seq data using attention-based neural networks border= 
 
Yuzhen Mao, Yen-Yi Lin, Nelson K Y Wong, Stanislav Volik, Funda Sar ...
 
 
 
scSemiGCN: boosting cell-type annotation from noise-resistant graph neural networks with extremely limited supervision border= 
 
Jue Yang, Weiwen Wang, Xiwen Zhang
 
 
 
Genetics and population analysis
 
 
 
 
MAGE: metafounders-assisted genomic estimation of breeding value, a novel additive-dominance single-step model in crossbreeding systems border= 
 
Yue Zhuo, Heng Du, ChenGuang Diao, WeiNing Li, Lei Zhou ...
 
 
 
The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population border= 
 
Hagai Levi, Ran Elkon, Ron Shamir
 
 
 
2dGBH: Two-dimensional group Benjamini'Hochberg procedure for false discovery rate control in two-way multiple testing of genomic data border= 
 
Lu Yang, Pei Wang, Jun Chen
 
 
 
High-dimensional quantile mediation analysis with application to a birth cohort study of mother'newborn pairs border= 
 
Haixiang Zhang, Xiumei Hong, Yinan Zheng, Lifang Hou, Cheng Zheng ...
 
 
 
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states 
 
Yongtao Guan, Daniel Levy
 
 
 
Systems biology
 
 
 
 
DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion border= 
 
Momoko Hamano, Toru Nakamura, Ryoku Ito, Yuki Shimada, Michio Iwata ...
 
 
 
Pitfalls of machine learning models for protein'protein interaction networks border=  
 
Loïc Lannelongue, Michael Inouye
 
 
 
Expanding the coverage of spatial proteomics: a machine learning approach border=  
 
Huangqingbo Sun, Jiayi Li, Robert F Murphy
 
 
 
Data and text mining
 
 
 
 
Multi-scale topology and position feature learning and relationship-aware graph reasoning for prediction of drug-related microbes border= 
 
Ping Xuan, Jing Gu, Hui Cui, Shuai Wang, Nakaguchi Toshiya ...
 
 
 
Interpreting protein abundance in Saccharomyces cerevisiae through relational learning border= 
 
Daniel Brunnsåker, Filip Kronström, Ievgeniia A Tiukova, Ross D King
 
 
 
GeneGPT: augmenting large language models with domain tools for improved access to biomedical information 
 
Qiao Jin, Yifan Yang, Qingyu Chen, Zhiyong Lu
 
 
 
Bioimage informatics
 
 
 
 
3D Optical Coherence Tomography image processing in BISCAP: characterization of biofilm structure and properties border= 
 
Diogo A C Narciso, Ana Pereira, Nuno O Dias, Manuel Monteiro, Luis F Melo ...
 
 
 
BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images border=  
 
Xinyuan Huang, Xiujuan Gao, Ling Fu
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
vcfpp: a C++ API for rapid processing of the variant call format border= 
 
Zilong Li
 
 
 
PanEffect: a pan-genome visualization tool for variant effects in maize 
 
Carson M Andorf, Olivia C Haley, Rita K Hayford, John L Portwood, II, Stephen Harding ...
 
 
 
NFTest: automated testing of Nextflow pipelines border=  
 
Yash Patel, Chenghao Zhu, Takafumi N Yamaguchi, Yuan Zhe Bugh, Mao Tian ...
 
 
 
PipeVal: light-weight extensible tool for file validation border=  
 
Yash Patel, Arpi Beshlikyan, Madison Jordan, Gina Kim, Aaron Holmes ...
 
 
 
Sequence analysis
 
 
 
 
TKSM: highly modular, user-customizable, and scalable transcriptomic sequencing long-read simulator border= 
 
Fatih KaraoÄŸlanoÄŸlu, Baraa Orabi, Ryan Flannigan, Cedric Chauve, Faraz Hach
 
 
 
GeNLP: a web tool for NLP-based exploration and prediction of microbial gene function border= 
 
Danielle Miller, Ofir Arias, David Burstein
 
 
 
HiPhase: jointly phasing small, structural, and tandem repeat variants from HiFi sequencing border= 
 
James M Holt, Christopher T Saunders, William J Rowell, Zev Kronenberg, Aaron M Wenger ...
 
 
 
pycofitness'Evaluating the fitness landscape of RNA and protein sequences border=  
 
Fabrizio Pucci, Mehari B Zerihun, Marianne Rooman, Alexander Schug
 
 
 
VariantDetective: an accurate all-in-one pipeline for detecting consensus bacterial SNPs and SVs border= 
 
Philippe Charron, Mingsong Kang
 
 
 
Gene expression
 
 
 
 
Scbean: a python library for single-cell multi-omics data analysis border= 
 
Haohui Zhang, Yuwei Wang, Bin Lian, Yiran Wang, Xingyi Li ...
 
 
 
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks border= 
 
Diego Mañanes, Inés Rivero-García, Carlos Relaño, Miguel Torres, David Sancho ...
 
 
 
Systems biology
 
 
 
 
SL-Miner: a web server for mining evidence and prioritization of cancer-specific synthetic lethality border= 
 
Xin Liu, Jieni Hu, Jie Zheng
 
 
 
Databases and ontologies
 
 
 
 
PERSEUS: an interactive and intuitive web-based tool for pedigree visualization border= 
 
Nicole Pradas, Federico Jurado-Ruiz, Carles Onielfa, Pere Arús, Maria José Aranzana
 
 
 
Correction
 
 
 
 
Correction to: GTExVisualizer: a web platform for supporting ageing studies border= 
 
 
 
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