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Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 11
 
November 2024
 
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Original Paper
 
 
 
 
Genome analysis
 
 
 
 
Generative haplotype prediction outperforms statistical methods for small variant detection in next-generation sequencing data border= 
 
Brendan O'Fallon, Ashini Bolia, Jacob Durtschi, Luobin Yang, Eric Fredrickson ...
 
 
 
GCI: a continuity inspector for complete genome assembly border=  
 
Quanyu Chen, Chentao Yang, Guojie Zhang, Dongya Wu
 
 
 
GEEES: inferring cell-specific gene'enhancer interactions from multi-modal single-cell data border= 
 
Shuyang Chen, Sündüz KeleÅŸ
 
 
 
BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data border= 
 
Congcong Hu, Yunxiao Li, Longhui Li, Naiqian Zhang, Xiaoqi Zheng
 
 
 
ADAPT: Analysis of Microbiome Differential Abundance by Pooling Tobit Models border=  
 
Mukai Wang, Simon Fontaine, Hui Jiang, Gen Li
 
 
 
 
Detecting transposable elements in long-read genomes using sTELLeR border= 
 
Kristine Bilgrav Saether, Jesper Eisfeldt
 
 
 
Sequence analysis
 
 
 
 
Addressing the antibody germline bias and its effect on language models for improved antibody design border= 
 
Tobias H Olsen, Iain H Moal, Charlotte M Deane
 
 
 
DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA border= 
 
Jiahao Yuan, Ziyi Wang, Zhuoyu Pan, Aohan Li, Zilong Zhang ...
 
 
 
Sitetack: a deep learning model that improves PTM prediction by using known PTMs border= 
 
Clair S Gutierrez, Alia A Kassim, Benjamin D Gutierrez, Ronald T Raines
 
 
 
InterLabelGO+: unraveling label correlations in protein function prediction border=  
 
Quancheng Liu, Chengxin Zhang, Lydia Freddolino
 
 
 
 
BIMSA: accelerating long sequence alignment using processing-in-memory border= 
 
Alejandro Alonso-Marín, Ivan Fernandez, Quim Aguado-Puig, Juan Gómez-Luna, Santiago Marco-Sola ...
 
 
 
p-IgGen: a paired antibody generative language model border=  
 
Oliver M Turnbull, Dino Oglic, Rebecca Croasdale-Wood, Charlotte M Deane
 
 
 
CompariPSSM: a PSSM'PSSM comparison tool for motif-binding determinant analysis border= 
 
Ifigenia Tsitsa, Izabella Krystkowiak, Norman E Davey
 
 
 
Expert-guided protein language models enable accurate and blazingly fast fitness prediction border= 
 
Céline Marquet, Julius Schlensok, Marina Abakarova, Burkhard Rost, Elodie Laine
 
 
 
Structural bioinformatics
 
 
 
 
Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins border= 
 
Javier González-Delgado, Pau Bernadó, Pierre Neuvial, Juan Cortés
 
 
 
EuDockScore: Euclidean graph neural networks for scoring protein'protein interfaces border= 
 
Matthew McFee, Jisun Kim, Philip M Kim
 
 
 
OpenDock: a pytorch-based open-source framework for protein'ligand docking and modelling border= 
 
Qiuyue Hu, Zechen Wang, Jintao Meng, Weifeng Li, Jingjing Guo ...
 
 
 
Protein structure alignment by Reseek improves sensitivity to remote homologs border= 
 
Robert C Edgar
 
 
 
Gene expression
 
 
 
 
PONYTA: prioritization of phenotype-related genes from mouse KO events using PU learning on a biological network border= 
 
Jun Hyeong Kim, Bonil Koo, Sun Kim
 
 
 
A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies border= 
 
Tasbiraha Athaya, Xiaoman Li, Haiyan Hu
 
 
 
A signal-diffusion-based unsupervised contrastive representation learning for spatial transcriptomics analysis border= 
 
Nan Chen, Xiao Yu, Weimin Li, Fangfang Liu, Yin Luo ...
 
 
 
Systems biology
 
 
 
 
PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server border= 
 
Yuying Shi, Botao Xu, Zhe Wang, Qitao Chen, Jie Chai ...
 
 
 
q2-metnet: QIIME2 package to analyse 16S rRNA data via high-quality metabolic reconstructions of the human gut microbiota border= 
 
Francesco Balzerani, Telmo Blasco, Sergio Pérez-Burillo, M Pilar Francino, José Á Rufián-Henares ...
 
 
 
Differential expression and co-expression reveal cell types relevant to genetic disorder phenotypes border= 
 
Sergio Alías-Segura, Florencio Pazos, Monica Chagoyen
 
 
 
Graphlet-based hyperbolic embeddings capture evolutionary dynamics in genetic networks border= 
 
Sam F L Windels, Daniel Tello Velasco, Mikhail Rotkevich, Noël Malod-Dognin, NataÅ¡a Pržulj
 
 
 
Target controllability: a feed-forward greedy algorithm in complex networks, meeting Kalman's rank condition border= 
 
Seyedeh Fatemeh Khezri, Ali Ebrahimi, Changiz Eslahchi
 
 
 
Optimizing multi-omics data imputation with NMF and GAN synergy border=  
 
Md Istiaq Ansari, Khandakar Tanvir Ahmed, Wei Zhang
 
 
 
RUCova: Removal of Unwanted Covariance in mass cytometry data border=  
 
Rosario Astaburuaga-García, Thomas Sell, Samet Mutlu, Anja Sieber, Kirsten Lauber ...
 
 
 
Genetics and population analysis
 
 
 
 
Detection and quantification of introgression using Bayesian inference based on conjugate priors border= 
 
Bastian Pfeifer, Durrell D Kapan, Sereina A Herzog
 
 
 
Quantifying defective and wild-type viruses from high-throughput RNA sequencing border= 
 
Juan C Muñoz-Sánchez, María J Olmo-Uceda, José-Ángel Oteo, Santiago F Elena
 
 
 
Data and text mining
 
 
 
 
Lifestyle factors in the biomedical literature: an ontology and comprehensive resources for named entity recognition border= 
 
Esmaeil Nourani, Mikaela Koutrouli, Yijia Xie, Danai Vagiaki, Sampo Pyysalo ...
 
 
 
k-nonical space: sketching with reverse complements border=  
 
Guillaume Marçais, C S Elder, Carl Kingsford
 
 
 
Improving ncRNA family prediction using multi-modal contrastive learning of sequence and structure border= 
 
Ruiting Xu, Dan Li, Wen Yang, Guohua Wang, Yang Li
 
 
 
Causal relationships between diseases mined from the literature improve the use of polygenic risk scores border= 
 
Sumyyah Toonsi, Iris Ivy Gauran, Hernando Ombao, Paul N Schofield, Robert Hoehndorf
 
 
 
Bioimage informatics
 
 
 
 
Deep coupled registration and segmentation of multimodal whole-brain images border= 
 
Tingting Han, Jun Wu, Pengpeng Sheng, Yuanyuan Li, ZaiYang Tao ...
 
 
 
Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis border= 
 
Zelin Li, Dongying Xie, Yiming Ma, Cunmin Zhao, Sicheng You ...
 
 
 
TRAITER: transformer-guided diagnosis and prognosis of heart failure using cell nuclear morphology and DNA damage marker border= 
 
Hiromu Hayashi, Toshiyuki Ko, Zhehao Dai, Kanna Fujita, Seitaro Nomura ...
 
 
 
Prediction of human O- linked glycosylation sites using stacked generalization and embeddings from pre-trained protein language model border= 
 
Subash Chandra Pakhrin, Neha Chauhan, Salman Khan, Jamie Upadhyaya, Moriah Rene Beck ...
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
Biologically-informed killer cell immunoglobulin-like receptor gene annotation tool 
 
Michael K B Ford, Ananth Hari, Qinghui Zhou, Ibrahim Numanagić, S Cenk Sahinalp
 
 
 
findGSEP: estimating genome size of polyploid species using k -mer frequencies border= 
 
Laiyi Fu, Yanxin Xie, Shunkang Ling, Ying Wang, Binzhong Wang ...
 
 
 
Cluster-efficient pangenome graph construction with nf-core/pangenome border=  
 
Simon Heumos, Michael L Heuer, Friederike Hanssen, Lukas Heumos, Andrea Guarracino ...
 
 
 
Xenomake: a pipeline for processing and sorting xenograft reads from spatial transcriptomic experiments border= 
 
Benjamin S Strope, Katherine E Pendleton, William Z Bowie, Gloria V Echeverria, Qian Zhu
 
 
 
BindCompare: a novel integrated protein'nucleic acid binding analysis platform border= 
 
Pranav Mahableshwarkar, Jasmine Shum, Mukulika Ray, Erica Larschan
 
 
 
Sequence analysis
 
 
 
 
quaqc: efficient and quick ATAC-seq quality control and filtering border= 
 
Benjamin J M Tremblay, Julia I Qüesta
 
 
 
Structural bioinformatics
 
 
 
 
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell border= 
 
Remco L van den Broek, Xabier Bello, Rebecca V Küpper, Gerard J P van Westen, Willem Jespers ...
 
 
 
R3DMCS: a web server for visualizing structural variation in RNA motifs across experimental 3D structures from the same organism or across species border= 
 
Sri Devan Appasamy, Craig L Zirbel
 
 
 
Gene expression
 
 
 
 
Collapsible tree: interactive web app to present collapsible hierarchies  
 
Yuan Gao, Rob Patro, Ph.D, Peng Jiang, Ph.D
 
 
 
ADTGP: correcting single-cell antibody sequencing data using Gaussian process regression border= 
 
Alex C H Liu, Steven M Chan
 
 
 
APAtizer: a tool for alternative polyadenylation analysis of RNA-Seq data border=  
 
Bruno Sousa, Maria Bessa, Filipa L de Mendonça, Pedro G Ferreira, Alexandra Moreira ...
 
 
 
Genetics and population analysis
 
 
 
 
AncestryGrapher toolkit: Python command-line pipelines to visualize global- and local- ancestry inferences from the RFMIX version 2 software border= 
 
Alessandro Lisi, Michael C Campbell
 
 
 
MR Corge: sensitivity analysis of Mendelian randomization based on the core gene hypothesis for polygenic exposures border= 
 
Wenmin Zhang, Chen-Yang Su, Satoshi Yoshiji, Tianyuan Lu
 
 
 
Pf-HaploAtlas: an interactive web app for spatiotemporal analysis of Plasmodium falciparum genes border= 
 
Chiyun Lee, Eyyüb S Ünlü, Nina F D White, Jacob Almagro-Garcia, Cristina Ariani ...
 
 
 
Systems biology
 
 
 
 
ENKIE: a package for predicting enzyme kinetic parameter values and their uncertainties border= 
 
Mattia G Gollub, Thierry Backes, Hans-Michael Kaltenbach, Jörg Stelling
 
 
 
Data and text mining
 
 
 
 
iSeq: an integrated tool to fetch public sequencing data border= 
 
Haoyu Chao, Zhuojin Li, Dijun Chen, Ming Chen
 
 
 
PubMed Computed Authors in 2024: an open resource of disambiguated author names in biomedical literature 
 
Shubo Tian, Qingyu Chen, Donald C Comeau, W John Wilbur, Zhiyong Lu
 
 
 
M2ara : unraveling metabolomic drug responses in whole-cell MALDI mass spectrometry bioassays border= 
 
Thomas Enzlein, Alexander Geisel, Carsten Hopf, Stefan Schmidt
 
 
 
PRONA: an R-package for Patient Reported Outcomes Network Analysis 
 
Brandon H Bergsneider, Orieta Celiku
 
 
 
Databases and ontologies
 
 
 
 
scToppR: a coding-friendly R interface to ToppGene border= 
 
Bryan Granger, Stefano Berto
 
 
 
ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox border= 
 
Norbert Deutsch, Zsuzsanna Dosztányi, István Csabai, Anna Medgyes-Horváth, Orsolya Anna Pipek ...
 
 
 
FungiFun3: systemic gene set enrichment analysis for fungal species border=  
 
Albert Garcia Lopez, Daniela Albrecht-Eckardt, Gianni Panagiotou, Sascha Schäuble
 
 
 
Bioimage informatics
 
 
 
 
MSIreg : an R package for unsupervised coregistration of mass spectrometry and H&E images border= 
 
Sai Srikanth Lakkimsetty, Andreas Weber, Kylie A Bemis, Verena Stehl, Peter Bronsert ...
 
 
 
Letter to the Editor
 
 
 
 
Genome analysis
 
 
 
 
Improving bioinformatics software quality through teamwork border= 
 
Katalin Ferenc, Ieva Rauluseviciute, Ladislav Hovan, Vipin Kumar, Marieke L Kuijjer ...
 
 
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