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New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 6
 
June 2024
 
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Review
 
 
 
 
Gene expression
 
 
 
 
Interpretable deep learning in single-cell omics border= 
 
Manoj M Wagle, Siqu Long, Carissa Chen, Chunlei Liu, Pengyi Yang
 
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
SAFPred: synteny-aware gene function prediction for bacteria using protein embeddings border= 
 
Aysun Urhan, Bianca-Maria Cosma, Ashlee M Earl, Abigail L Manson, Thomas Abeel
 
 
 
AmplificationTimeR: an R package for timing sequential amplification events border=  
 
G Maria Jakobsdottir, Stefan C Dentro, Robert G Bristow, David C Wedge
 
 
 
Subtype-MGTP: a cancer subtype identification framework based on multi-omics translation border= 
 
Minzhu Xie, Yabin Kuang, Mengyun Song, Ergude Bao
 
 
 
RNA m6A detection using raw current signals and basecalling errors from Nanopore direct RNA sequencing reads border= 
 
Peng Ni, Jinrui Xu, Zeyu Zhong, Feng Luo, Jianxin Wang
 
 
 
 
 
Sequence analysis
 
 
 
 
Incorporating temporal dynamics of mutations to enhance the prediction capability of antiretroviral therapy's outcome for HIV-1 border= 
 
Giulia Di Teodoro, Martin Pirkl, Francesca Incardona, Ilaria Vicenti, Anders Sönnerborg ...
 
 
 
MSModDetector: a tool for detecting mass shifts and post-translational modifications in individual ion mass spectrometry data border= 
 
Marjan Faizi, Ryan T Fellers, Dan Lu, Bryon S Drown, Ashwini Jambhekar ...
 
 
 
Readon: a novel algorithm to identify read-through transcripts with long-read sequencing data border= 
 
Siang Chen, Hao Wang, Dongdong Zhang, Runsheng Chen, Jianjun Luo
 
 
 
HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer border= 
 
Xiaopeng Xu, Chencheng Xu, Wenjia He, Lesong Wei, Haoyang Li ...
 
 
 
Phylogenetics
 
 
 
 
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach border= 
 
Yueyu Jiang, Daniel McDonald, Daniela Perry, Rob Knight, Siavash Mirarab
 
 
 
 
 
Structural bioinformatics
 
 
 
 
FMCA-DTI: a fragment-oriented method based on a multihead cross attention mechanism to improve drug'target interaction prediction border= 
 
Qi Zhang, Le Zuo, Ying Ren, Siyuan Wang, Wenfa Wang ...
 
 
 
OLB-AC: toward optimizing ligand bioactivities through deep graph learning and activity cliffs border= 
 
Yueming Yin, Haifeng Hu, Jitao Yang, Chun Ye, Wilson Wen Bin Goh ...
 
 
 
Gene expression
 
 
 
 
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation border= 
 
Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min ...
 
 
 
HE2Gene: image-to-RNA translation via multi-task learning for spatial transcriptomics data border= 
 
Xingjian Chen, Jiecong Lin, Yuchen Wang, Weitong Zhang, Weidun Xie ...
 
 
 
Supervised learning of enhancer'promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning border= 
 
Dylan Barth, Richard Van, Jonathan Cardwell, Mira V Han
 
 
 
scCross: efficient search for rare subpopulations across multiple single-cell samples border= 
 
Alexander Gerniers, Siegfried Nijssen, Pierre Dupont
 
 
 
Genetics and population analysis
 
 
 
 
SNP-slice resolves mixed infections: simultaneously unveiling strain haplotypes and linking them to hosts border= 
 
Nianqiao Ju, Jiawei Liu, Qixin He
 
 
 
Systems biology
 
 
 
 
Drug'target interaction predictions with multi-view similarity network fusion strategy and deep interactive attention mechanism border= 
 
Wei Song, Lewen Xu, Chenguang Han, Zhen Tian, Quan Zou
 
 
 
spillR : spillover compensation in mass cytometry data border= 
 
Marco Guazzini, Alexander G Reisach, Sebastian Weichwald, Christof Seiler
 
 
 
Data and text mining
 
 
 
 
Improving the performance and interpretability on medical datasets using graphical ensemble feature selection border= 
 
Enzo Battistella, Dina Ghiassian, Albert-László Barabási
 
 
 
TARO: tree-aggregated factor regression for microbiome data integration border=  
 
Aditya K Mishra, Iqbal Mahmud, Philip L Lorenzi, Robert R Jenq, Jennifer A Wargo ...
 
 
 
DEAttentionDTA: protein'ligand binding affinity prediction based on dynamic embedding and self-attention border= 
 
Xiying Chen, Jinsha Huang, Tianqiao Shen, Houjin Zhang, Li Xu ...
 
 
 
MCDHGN: heterogeneous network-based cancer driver gene prediction and interpretability analysis border= 
 
Lexiang Wang, Jingli Zhou, Xuan Wang, Yadong Wang, Junyi Li
 
 
 
Computing linkage disequilibrium aware genome embeddings using autoencoders border=  
 
Gizem TaÅŸ, Timo Westerdijk, Eric Postma, Wouter van Rheenen, Mark K Bakker ...
 
 
 
Bioimage informatics
 
 
 
 
CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm border= 
 
Teng-Yu Lin, Szu-Chi Chung
 
 
 
GammaGateR: semi-automated marker gating for single-cell multiplexed imaging border=  
 
Jiangmei Xiong, Harsimran Kaur, Cody N Heiser, Eliot T McKinley, Joseph T Roland ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models border= 
 
Ketrin Gjoni, Katherine S Pollard
 
 
 
Mariner: explore the Hi-Cs border= 
 
Eric S Davis, Sarah M Parker, Nicole E Kramer, J P Flores, Manjari Kiran ...
 
 
 
Figeno: multi-region genomic figures with long-read support border=  
 
Etienne Sollier, Jessica Heilmann, Clarissa Gerhauser, Michael Scherer, Christoph Plass ...
 
 
 
Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases border= 
 
Francesco Gualdi, Baldomero Oliva, Janet Piñero
 
 
 
Sequence analysis
 
 
 
 
SWGTS'a platform for stream-based host DNA depletion border= 
 
Philipp Spohr, Max Ried, Laura Kühle, Alexander Dilthey
 
 
 
Flexible parsing, interpretation, and editing of technical sequences with splitcode border= 
 
Delaney K Sullivan, Lior Pachter
 
 
 
GenoFig: a user-friendly application for the visualization and comparison of genomic regions border= 
 
Maxime Branger, Sébastien O Leclercq
 
 
 
Structural bioinformatics
 
 
 
 
MolDy: molecular dynamics simulation made easy border= 
 
Mohd Imran Khan, Sheetal Pathania, Mohammed W Al-Rabia, Abdul S Ethayathulla, Mohammad Imran Khan ...
 
 
 
MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2 border= 
 
Ho Yeung Chim, Arne Elofsson
 
 
 
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments border= 
 
Sebastian Bittrich, Joan Segura, Jose M Duarte, Stephen K Burley, Yana Rose
 
 
 
Gene expression
 
 
 
 
RiboGraph: an interactive visualization system for ribosome profiling data at read length resolution border= 
 
Jonathan Chacko, Hakan Ozadam, Can Cenik
 
 
 
Ragas: integration and enhanced visualization for single cell subcluster analysis border= 
 
Uthra Balaji, Juan Rodríguez-Alcázar, Preetha Balasubramanian, Cynthia Smitherman, Jeanine Baisch ...
 
 
 
Genetics and population analysis
 
 
 
 
snpAIMeR: R package for evaluating ancestry informative marker contributions in non-model population diagnostics border= 
 
Kim L Vertacnik, Oksana V Vernygora, Julian R Dupuis
 
 
 
Systems biology
 
 
 
 
ReactomeGSA: new features to simplify public data reuse border= 
 
Alexander Grentner, Eliot Ragueneau, Chuqiao Gong, Adrian Prinz, Sabina Gansberger ...
 
 
 
PathwayNexus: a tool for interactive metabolic data analysis border=  
 
Philipp Eberhard, Martin Kern, Michael Aichem, Hanna Borlinghaus, Karsten Klein ...
 
 
 
bnglViz: online visualization of rule-based models border=  
 
Noah Liguori-Bills, Michael L Blinov
 
 
 
gMCSpy: efficient and accurate computation of genetic minimal cut sets in Python border= 
 
Carlos J Rodriguez-Flores, Naroa Barrena, Danel Olaverri-Mendizabal, Idoia Ochoa, Luis V Valcárcel ...
 
 
 
MetaboReport: from metabolomics data analysis to comprehensive reporting border=  
 
Yonghui Dong, Sergey Malitsky
 
 
 
Data and text mining
 
 
 
 
Bigtools: a high-performance BigWig and BigBed library in Rust border= 
 
Jack D Huey, Nezar Abdennur
 
 
 
biotextgraph : graphical summarization of functional similarities from textual information border= 
 
Noriaki Sato, Yao-zhong Zhang, Zuguang Gu, Seiya Imoto
 
 
 
DDN3.0: determining significant rewiring of biological network structure with differential dependency networks border= 
 
Yi Fu, Yingzhou Lu, Yizhi Wang, Bai Zhang, Zhen Zhang ...
 
 
 
Databases and ontologies
 
 
 
 
KRAGEN: a knowledge graph-enhanced RAG framework for biomedical problem solving using large language models border= 
 
Nicholas Matsumoto, Jay Moran, Hyunjun Choi, Miguel E Hernandez, Mythreye Venkatesan ...
 
 
 
Correction
 
 
 
 
Correction to: For antibody sequence generative modeling, mixture models may be all you need border= 
 
 
 
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