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New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 3
 
March 2024
 
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Review
 
 
 
 
Genetics and population analysis
 
 
 
 
Tutorial on survival modeling with applications to omics data border= 
 
Zhi Zhao, John Zobolas, Manuela Zucknick, Tero Aittokallio
 
 
 
Original Papers
 
 
 
 
Genome analysis
 
 
 
 
ViTAL: Vision TrAnsformer based Low coverage SARS-CoV-2 lineage assignment border= 
 
Zuher Jahshan, Leonid Yavits
 
 
 
ARGprofiler'a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets border= 
 
Hannah-Marie Martiny, Nikiforos Pyrounakis, Thomas N Petersen, Oksana Lukjan─Źenko, Frank M Aarestrup ...
 
 
 
Ribotin: automated assembly and phasing of rDNA morphs border=  
 
Mikko Rautiainen
 
 
 
A compressive seeding algorithm in conjunction with reordering-based compression border= 
 
Fahu Ji, Qian Zhou, Jue Ruan, Zexuan Zhu, Xianming Liu
 
 
 
 
Identifying TAD-like domains on single-cell Hi-C data by graph embedding and changepoint detection border= 
 
Erhu Liu, Hongqiang Lyu, Yuan Liu, Laiyi Fu, Xiaoliang Cheng ...
 
 
 
Uncovering genetic associations in the human diseasome using an endophenotype-augmented disease network border= 
 
Jakob Woerner, Vivek Sriram, Yonghyun Nam, Anurag Verma, Dokyoon Kim
 
 
 
EpiVar Browser: advanced exploration of epigenomics data under controlled access border= 
 
David R Lougheed, Hanshi Liu, Katherine A Aracena, Romain Grégoire, Alain Pacis ...
 
 
 
Sequence analysis
 
 
 
 
Flexiplex: a versatile demultiplexer and search tool for omics data border= 
 
Oliver Cheng, Min Hao Ling, Changqing Wang, Shuyi Wu, Matthew E Ritchie ...
 
 
 
Exact global alignment using A* with chaining seed heuristic and match pruning border= 
 
Ragnar Groot Koerkamp, Pesho Ivanov
 
 
 
 
A dual-rule encoding DNA storage system using chaotic mapping to control GC content border= 
 
Xuncai Zhang, Baonan Qi, Ying Niu
 
 
 
PySNV for complex intra-host variation detection border=  
 
Liandong Li, Haoyi Fu, Wentai Ma, Mingkun Li
 
 
 
Insights into the inner workings of transformer models for protein function prediction border= 
 
Markus Wenzel, Erik Grüner, Nils Strodthoff
 
 
 
NPSV-deep: a deep learning method for genotyping structural variants in short read genome sequencing data border= 
 
Michael D Linderman, Jacob Wallace, Alderik van der Heyde, Eliza Wieman, Daniel Brey ...
 
 
 
MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life border= 
 
Jose L Figueroa III, Eliza Dhungel, Madeline Bellanger, Cory R Brouwer, Richard Allen White III
 
 
 
Lambda3: homology search for protein, nucleotide, and bisulfite-converted sequences border= 
 
Hannes Hauswedell, Sara Hetzel, Simon G Gottlieb, Helene Kretzmer, Alexander Meissner ...
 
 
 
AACFlow: an end-to-end model based on attention augmented convolutional neural network and flow-attention mechanism for identification of anticancer peptides border= 
 
Shengli Zhang, Ya Zhao, Yunyun Liang
 
 
 
Phylogenetics
 
 
 
 
Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation border= 
 
David Ferreiro, Catarina Branco, Miguel Arenas
 
 
 
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS border= 
 
Emese I Végh, Katerina Douka
 
 
 
Structural bioinformatics
 
 
 
 
RT-Transformer: retention time prediction for metabolite annotation to assist in metabolite identification border= 
 
Jun Xue, Bingyi Wang, Hongchao Ji, WeiHua Li
 
 
 
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space border= 
 
Hamza Biyuzan, Mohamed-Akram Masrour, Lucas Grandmougin, Frédéric Payan, Dominique Douguet
 
 
 
Optimizing representations for integrative structural modeling using Bayesian model selection border= 
 
Shreyas Arvindekar, Aditi S Pathak, Kartik Majila, Shruthi Viswanath
 
 
 
Utilizing the scale-invariant feature transform algorithm to align distance matrices facilitates systematic protein structure comparison border= 
 
Zhengyang Guo, Yang Wang, Guangshuo Ou
 
 
 
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs border= 
 
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
 
 
 
Graph-theoretical prediction of biological modules in quaternary structures of large protein complexes border= 
 
Florian J Gisdon, Mariella Zunker, Jan Niclas Wolf, Kai Prüfer, Jörg Ackermann ...
 
 
 
iNGNN-DTI: prediction of drug'target interaction with interpretable nested graph neural network and pretrained molecule models border= 
 
Yan Sun, Yan Yi Li, Carson K Leung, Pingzhao Hu
 
 
 
AbFlex: designing antibody complementarity determining regions with flexible CDR definition border= 
 
Woosung Jeon, Dongsup Kim
 
 
 
Gene expression
 
 
 
 
Information-incorporated gene network construction with FDR control border= 
 
Hao Wang, Yumou Qiu, Hongqing Guo, Yanhai Yin, Peng Liu
 
 
 
BERMAD: batch effect removal for single-cell RNA-seq data using a multi-layer adaptation autoencoder with dual-channel framework border= 
 
Xiangxin Zhan, Yanbin Yin, Han Zhang
 
 
 
Uncertainty-aware single-cell annotation with a hierarchical reject option border=  
 
Lauren Theunissen, Thomas Mortier, Yvan Saeys, Willem Waegeman
 
 
 
Systems biology
 
 
 
 
Incorporating temporal information during feature engineering bolsters emulation of spatio-temporal emergence border= 
 
Jason Y Cain, Jacob I Evarts, Jessica S Yu, Neda Bagheri
 
 
 
Data and text mining
 
 
 
 
LAVASET: Latent Variable Stochastic Ensemble of Trees. An ensemble method for correlated datasets with spatial, spectral, and temporal dependencies border= 
 
Melpomeni Kasapi, Kexin Xu, Timothy M D Ebbels, Declan P O'Regan, James S Ware ...
 
 
 
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning border= 
 
J Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L Harris, Marcin P Joachimiak ...
 
 
 
MARS: a motif-based autoregressive model for retrosynthesis prediction border=  
 
Jiahan Liu, Chaochao Yan, Yang Yu, Chan Lu, Junzhou Huang ...
 
 
 
Databases and ontologies
 
 
 
 
HIResist: a database of HIV-1 resistance to broadly neutralizing antibodies border= 
 
Milind Misra, Jeffy Jeffy, Charis Liao, Stephanie Pickthorn, Kshitij Wagh ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization border= 
 
Guillermo Dufort y Álvarez, Martí Xargay-Ferrer, Alba Pagès-Zamora, Idoia Ochoa
 
 
 
AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification border= 
 
Jung Kim, Ammar S Naqvi, Ryan J Corbett, Rebecca S Kaufman, Zalman Vaksman ...
 
 
 
Digger: directed annotation of immunoglobulin and T cell receptor V, D, and J gene sequences and assemblies border= 
 
William D Lees, Swati Saha, Gur Yaari, Corey T Watson
 
 
 
Sequence analysis
 
 
 
 
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow border= 
 
Yiyang Yu, Shivani Muthukumar, Peter K Koo
 
 
 
Nanometa Live: a user-friendly application for real-time metagenomic data analysis and pathogen identification border= 
 
Kristofer Sandås, Jacob Lewerentz, Edvin Karlsson, Linda Karlsson, David Sundell ...
 
 
 
Fast and scalable querying of eukaryotic linear motifs with gget elm border=  
 
Laura Luebbert, Chi Hoang, Manjeet Kumar, Lior Pachter
 
 
 
ElemeNT 2023: an enhanced tool for detection and curation of core promoter elements border= 
 
Orit Adato, Anna Sloutskin, Hodaya Komemi, Ian Brabb, Sascha Duttke ...
 
 
 
Structural bioinformatics
 
 
 
 
Rapid generation of high-quality structure figures for publication with PyMOL-PUB border= 
 
Yuting Chen, Haoling Zhang, Wen Wang, Yue Shen, Zhi Ping
 
 
 
Gene expression
 
 
 
 
GPro: generative AI-empowered toolkit for promoter design border= 
 
Haochen Wang, Qixiu Du, Ye Wang, Hanwen Xu, Zheng Wei ...
 
 
 
KaMRaT: a C++ toolkit for k -mer count matrix dimension reduction border= 
 
Haoliang Xue, Mélina Gallopin, Camille Marchet, Ha N Nguyen, Yunfeng Wang ...
 
 
 
vizAPA: visualizing dynamics of alternative polyadenylation from bulk and single-cell data border= 
 
Xingyu Bi, Wenbin Ye, Xin Cheng, Ning Yang, Xiaohui Wu
 
 
 
ICELLNET v2: a versatile method for cell'cell communication analysis from human transcriptomic data border= 
 
Lucile Massenet-Regad, Vassili Soumelis
 
 
 
SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments 
 
Chitrasen Mohanty, Aman Prasad, Lingxin Cheng, Lisa M Arkin, Bridget E Shields ...
 
 
 
Systems biology
 
 
 
 
Shu: visualization of high-dimensional biological pathways border= 
 
Jorge Carrasco Muriel, Nicholas Cowie, Shannara Taylor Parkins, Marjan Mansouvar, Teddy Groves ...
 
 
 
Data and text mining
 
 
 
 
preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology border= 
 
Arik Ermshaus, Michael Piechotta, Gina Rüter, Ulrich Keilholz, Ulf Leser ...
 
 
 
imputomics: web server and R package for missing values imputation in metabolomics data border= 
 
Jarosław Chilimoniuk, Krystyna Grzesiak, Jakub Kała, Dominik Nowakowski, Adam Krętowski ...
 
 
 
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution border= 
 
Chiung-Ting Wu, Dongping Du, Lulu Chen, Rujia Dai, Chunyu Liu ...
 
 
 
Bioimage informatics
 
 
 
 
SST-editing: in silico spatial transcriptomic editing at single-cell resolution border= 
 
Jiqing Wu, Viktor H Koelzer
 
 
 
pyM2 aia: Python interface for mass spectrometry imaging with focus on deep learning border= 
 
Jonas Cordes, Thomas Enzlein, Carsten Hopf, Ivo Wolf
 
 
 
Correction
 
 
 
 
Correction to: OncoThreads: visualization of large-scale longitudinal cancer molecular data border= 
 
 
 
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