Subject: Bioinformatics Table of Contents for December 2024 Oxford Academic
 
 
 
Oxford Academic
 
 
 
 
New issue alert
 
 
 
 
Bioinformatics  
Volume 40 Issue 12
 
December 2024
 
button-issue.png
 
 
Original Paper
 
 
 
 
Genome analysis
 
 
 
 
Tiberius: end-to-end deep learning with an HMM for gene prediction border= 
 
Lars Gabriel, Felix Becker, Katharina J Hoff, Mario Stanke
 
 
 
Micro-DeMix: a mixture beta-multinomial model for investigating the heterogeneity of the stool microbiome compositions border= 
 
Ruoqian Liu, Yue Wang, Dan Cheng
 
 
 
Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C data border= 
 
Jun Zhang, Fan Nie, Feng Luo, Jianxin Wang
 
 
 
Identification and annotation of centromeric hypomethylated regions with CDR-Finder border= 
 
Francesco Kumara Mastrorosa, Keisuke K Oshima, Allison N Rozanski, William T Harvey, Evan E Eichler ...
 
 
 
Sequence analysis
 
 
 
 
Predicting the subcellular location of prokaryotic proteins with DeepLocPro border= 
 
Jaime Moreno, Henrik Nielsen, Ole Winther, Felix Teufel
 
 
 
 
HAlign 4: a new strategy for rapidly aligning millions of sequences border= 
 
Tong Zhou, Pinglu Zhang, Quan Zou, Wu Han
 
 
 
BWT construction and search at the terabase scale border=  
 
Heng Li
 
 
 
A BLAST from the past: revisiting blastp's E-value border= 
 
Yang Young Lu, William Stafford Noble, Uri Keich
 
 
 
Phylogenetics
 
 
 
 
Sparse Neighbor Joining: rapid phylogenetic inference using a sparse distance matrix border= 
 
Semih Kurt, Alexandre Bouchard-Côté, Jens Lagergren
 
 
 
spread.gl: visualizing pathogen dispersal in a high-performance browser application border= 
 
Yimin Li, Nena Bollen, Samuel L Hong, Marius Brusselmans, Fabiana Gambaro ...
 
 
 
 
 
Structural bioinformatics
 
 
 
 
Improved prediction of post-translational modification crosstalk within proteins using DeepPCT border= 
 
Yu-Xiang Huang, Rong Liu
 
 
 
Accurate and transferable drug'target interaction prediction with DrugLAMP border=  
 
Zhengchao Luo, Wei Wu, Qichen Sun, Jinzhuo Wang
 
 
 
Gene expression
 
 
 
 
Mutual information for detecting multi-class biomarkers when integrating multiple bulk or single-cell transcriptomic studies border= 
 
Jian Zou, Zheqi Li, Neil Carleton, Steffi Oesterreich, Adrian V Lee ...
 
 
 
Virtual tissue expression analysis border=  
 
Jakob Simeth, Paul Hüttl, Marian Schön, Zahra Nozari, Michael Huttner ...
 
 
 
Systems biology
 
 
 
 
Dynamic modelling of signalling pathways when ordinary differential equations are not feasible border= 
 
Timo Rachel, Eva Brombacher, Svenja Wöhrle, Olaf Groß, Clemens Kreutz
 
 
 
OneSC: a computational platform for recapitulating cell state transitions border=  
 
Da Peng, Patrick Cahan
 
 
 
DrugRepPT: a deep pretraining and fine-tuning framework for drug repositioning based on drug's expression perturbation and treatment effectiveness border= 
 
Shuyue Fan, Kuo Yang, Kezhi Lu, Xin Dong, Xianan Li ...
 
 
 
Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides border= 
 
Sean J McIlwain, Anna Hoefges, Amy K Erbe, Paul M Sondel, Irene M Ong
 
 
 
Sensitivities in protein allocation models reveal distribution of metabolic capacity and flux control border= 
 
Samira van den Bogaard, Pedro A Saa, Tobias B Alter
 
 
 
Fast polypharmacy side effect prediction using tensor factorization border=  
 
Oliver Lloyd, Yi Liu, Tom R Gaunt
 
 
 
DeepRSMA: a cross-fusion-based deep learning method for RNA'small molecule binding affinity prediction border= 
 
Zhijian Huang, Yucheng Wang, Song Chen, Yaw Sing Tan, Lei Deng ...
 
 
 
Data and text mining
 
 
 
 
FAPM: functional annotation of proteins using multimodal models beyond structural modeling border= 
 
Wenkai Xiang, Zhaoping Xiong, Huan Chen, Jiacheng Xiong, Wei Zhang ...
 
 
 
Knowledge mining of brain connectivity in massive literature based on transfer learning border= 
 
Xiaokang Chai, Sile An, Simeng Chen, Wenwei Li, Zhao Feng ...
 
 
 
HBFormer: a single-stream framework based on hybrid attention mechanism for identification of human-virus protein'protein interactions border= 
 
Liyuan Zhang, Sicong Wang, Yadong Wang, Tianyi Zhao
 
 
 
Bioimage informatics
 
 
 
 
FEHAT: efficient, large scale and automated heartbeat detection in Medaka fish embryos border= 
 
Marcio Soares Ferreira, Sebastian Stricker, Tomas Fitzgerald, Jack Monahan, Fanny Defranoux ...
 
 
 
AltGosling: automatic generation of text descriptions for accessible genomics data visualization border= 
 
Thomas C Smits, Sehi L'Yi, Andrew P Mar, Nils Gehlenborg
 
 
 
Applications Note
 
 
 
 
Genome analysis
 
 
 
 
Damsel: analysis and visualisation of DamID sequencing in R border= 
 
Caitlin G Page, Andrew Londsdale, Katrina A Mitchell, Jan Schröder, Kieran F Harvey ...
 
 
 
easySCF: a tool for enhancing interoperability between R and Python for efficient single-cell data analysis border= 
 
Haoyun Zhang, Wentao Zhang, Shuai Zhao, Guangyu Xu, Yi Shen ...
 
 
 
JARVIS3: an efficient encoder for genomic data border=  
 
Maria J P Sousa, Armando J Pinho, Diogo Pratas
 
 
 
Panacus: fast and exact pangenome growth and core size estimation border=  
 
Luca Parmigiani, Erik Garrison, Jens Stoye, Tobias Marschall, Daniel Doerr
 
 
 
lefser: implementation of metagenomic biomarker discovery tool, LEfSe, in R border= 
 
Asya Khleborodova, Samuel D Gamboa-Tuz, Marcel Ramos, Nicola Segata, Levi Waldron ...
 
 
 
Sequence analysis
 
 
 
 
Pod5Viewer: a GUI for inspecting raw nanopore sequencing data border= 
 
Vincent Dietrich, Nicolò Alagna, Mark Helm, Susanne Gerber, Tamer Butto
 
 
 
ViraLM: empowering virus discovery through the genome foundation model border=  
 
Cheng Peng, Jiayu Shang, Jiaojiao Guan, Donglin Wang, Yanni Sun
 
 
 
Polyphonia: detecting inter-sample contamination in viral genomic sequencing data border= 
 
Lydia A Krasilnikova, Christopher H Tomkins-Tinch, Alton C Gayton, Stephen F Schaffner, Sabrina T Dobbins ...
 
 
 
Structural bioinformatics
 
 
 
 
STRPsearch: fast detection of structured tandem repeat proteins border= 
 
Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari ...
 
 
 
Afpdb: an efficient structure manipulation package for AI protein design border=  
 
Yingyao Zhou, Jiayi Cox, Bin Zhou, Steven Zhu, Yang Zhong ...
 
 
 
Gene expression
 
 
 
 
Gene count estimation with pytximport enables reproducible analysis of bulk RNA sequencing data in Python border= 
 
Malte Kuehl, Milagros N Wong, Nicola Wanner, Stefan Bonn, Victor G Puelles
 
 
 
VSS-Hi-C: variance-stabilized signals for chromatin contacts border=  
 
Neda Shokraneh Kenari, Faezeh Bayat, Maxwell W Libbrecht
 
 
 
GUEST : an R package for handling estimation of graphical structure and multiclassification for error-prone gene expression data border= 
 
Li-Pang Chen, Hui-Shan Tsao
 
 
 
Systems biology
 
 
 
 
FastTENET: an accelerated TENET algorithm based on manycore computing in Python border= 
 
Rakbin Sung, Hyeonkyu Kim, Junil Kim, Daewon Lee
 
 
 
PhosX: data-driven kinase activity inference from phosphoproteomics experiments border= 
 
Alessandro Lussana, Sophia Müller-Dott, Julio Saez-Rodriguez, Evangelia Petsalaki
 
 
 
Data and text mining
 
 
 
 
Facilitating phenotyping from clinical texts: the medkit library border= 
 
Antoine Neuraz, Ghislain Vaillant, Camila Arias, Olivier Birot, Kim-Tam Huynh ...
 
 
 
LmRaC: a functionally extensible tool for LLM interrogation of user experimental results border= 
 
Douglas B Craig, Sorin Drăghici
 
 
 
DeepDR: a deep learning library for drug response prediction border=  
 
Zhengxiang Jiang, Pengyong Li
 
 
 
OpenVariant: a toolkit to parse and operate multiple input file formats border=  
 
David Martínez-Millán, Federica Brando, Miguel L. Grau, Mònica Sánchez-Guixé, Carlos López-Elorduy ...
 
 
 
STRprofiler: efficient comparisons of short tandem repeat profiles for biomedical model authentication border= 
 
Jared M Andrews, Michael W Lloyd, Steven B Neuhauser, Margaret Bundy, Emily L Jocoy ...
 
 
 
Bioimage informatics
 
 
 
 
CVR-BBI: an open-source VR platform for multi-user collaborative brain to brain interfaces border= 
 
Di Liu, Yina Wei
 
 
Unsubscribe       Manage email alerts
 
Written requests to unsubscribe can be sent to: Journals Marketing, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK.

Our Privacy Policy sets out how Oxford University Press handles your personal information.

The content of this email is protected by copyright.
 
Oxford University Press
 
 
                                 



This email is intended for bionet@evol.mcmaster.ca.