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Oxford Academic
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Volume 40 Issue 5
May 2024
GradHC: highly reliable gradual hash-based clustering for DNA storage systems
Dvir Ben Shabat
,
Adar Hadad
,
Avital Boruchovsky
,
Eitan Yaakobi
Revisiting drug'protein interaction prediction: a novel global'local perspective
Zhecheng Zhou
,
Qingquan Liao
,
Jinhang Wei
,
Linlin Zhuo
,
Xiaonan Wu
...
CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics
Semih Kurt
,
Mandi Chen
,
Hosein Toosi
,
Xinsong Chen
,
Camilla Engblom
...
Original Paper
Genome analysis
A data-adaptive methods in detecting exogenous methyltransferase accessible chromatin in human genome using nanopore sequencing
Kailing Tu
,
Xuemei Li
,
Qilin Zhang
,
Wei Huang
,
Dan Xie
wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication
Hengchi Chen
,
Arthur Zwaenepoel
,
Yves Van de Peer
MUSE-XAE: MUtational Signature Extraction with eXplainable AutoEncoder enhances tumour types classification
Corrado Pancotti
,
Cesare Rollo
,
Francesco Codicè
,
Giovanni Birolo
,
Piero Fariselli
...
Sequence Analysis
LMCrot: an enhanced protein crotonylation site predictor by leveraging an interpretable window-level embedding from a transformer-based protein language model
Pawel Pratyush
,
Soufia Bahmani
,
Suresh Pokharel
,
Hamid D Ismail
,
Dukka B KC
For antibody sequence generative modeling, mixture models may be all you need
Jonathan Parkinson
,
Wei Wang
RecGraph: recombination-aware alignment of sequences to variation graphs
Jorge Avila Cartes
,
Paola Bonizzoni
,
Simone Ciccolella
,
Gianluca Della Vedova
,
Luca Denti
...
DeepPPAPredMut: deep ensemble method for predicting the binding affinity change in protein'protein complexes upon mutation
Rahul Nikam
,
Sherlyn Jemimah
,
M Michael Gromiha
DeepAVP-TPPred: identification of antiviral peptides using transformed image-based localized descriptors and binary tree growth algorithm
Matee Ullah
,
Shahid Akbar
,
Ali Raza
,
Quan Zou
Integrated convolution and self-attention for improving peptide toxicity prediction
Shihu Jiao
,
Xiucai Ye
,
Tetsuya Sakurai
,
Quan Zou
,
Ruijun Liu
Structural bioinformatics
AbLEF: antibody language ensemble fusion for thermodynamically empowered property predictions
Zachary A Rollins
,
Talal Widatalla
,
Andrew Waight
,
Alan C Cheng
,
Essam Metwally
MEG-PPIS: a fast protein'protein interaction site prediction method based on multi-scale graph information and equivariant graph neural network
Hongzhen Ding
,
Xue Li
,
Peifu Han
,
Xu Tian
,
Fengrui Jing
...
Chainsaw: protein domain segmentation with fully convolutional neural networks
Jude Wells
,
Alex Hawkins-Hooker
,
Nicola Bordin
,
Ian Sillitoe
,
Brooks Paige
...
Gene expression
Peptide set test: a peptide-centric strategy to infer differentially expressed proteins
Junmin Wang
,
Steven Novick
scPRAM accurately predicts single-cell gene expression perturbation response based on attention mechanism
Qun Jiang
,
Shengquan Chen
,
Xiaoyang Chen
,
Rui Jiang
scTPC: a novel semisupervised deep clustering model for scRNA-seq data
Yushan Qiu
,
Lingfei Yang
,
Hao Jiang
,
Quan Zou
Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data
Marco Stock
,
Niclas Popp
,
Jonathan Fiorentino
,
Antonio Scialdone
Scalable integration of multiomic single-cell data using generative adversarial networks
Valentina Giansanti
,
Francesca Giannese
,
Oronza A Botrugno
,
Giorgia Gandolfi
,
Chiara Balestrieri
...
Inferring gene regulatory networks from single-cell transcriptomics based on graph embedding
Yanglan Gan
,
Jiacheng Yu
,
Guangwei Xu
,
Cairong Yan
,
Guobing Zou
Genetics and population analysis
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals
Wenmin Zhang
,
Tianyuan Lu
,
Robert Sladek
,
Yue Li
,
Hamed Najafabadi
...
Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape
Andreas Wagner
Systems biology
Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS
Remi Trimbour
,
Ina Maria Deutschmann
,
Laura Cantini
NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population
Anja Mösch
,
Filippo Grazioli
,
Pierre Machart
,
Brandon Malone
A supervised Bayesian factor model for the identification of multi-omics signatures
Jeremy P Gygi
,
Anna Konstorum
,
Shrikant Pawar
,
Edel Aron
,
Steven H Kleinstein
...
BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities
Telmo Blasco
,
Francesco Balzerani
,
Luis V Valcárcel
,
Pedro Larrañaga
,
Concha Bielza
...
fastCCLasso: a fast and efficient algorithm for estimating correlation matrix from compositional data
Shen Zhang
,
Huaying Fang
,
Tao Hu
Bayesian modelling of time series data (BayModTS)'a FAIR workflow to process sparse and highly variable data
Sebastian Höpfl
,
Mohamed Albadry
,
Uta Dahmen
,
Karl-Heinz Herrmann
,
Eva Marie Kindler
...
BindingSiteDTI: differential-scale binding site modelling for drug'target interaction prediction
Feng Pan
,
Chong Yin
,
Si-Qi Liu
,
Tao Huang
,
Zhaoxiang Bian
...
DiSMVC: a multi-view graph collaborative learning framework for measuring disease similarity
Hang Wei
,
Lin Gao
,
Shuai Wu
,
Yina Jiang
,
Bin Liu
GateMeClass: Gate Mining and Classification of cytometry data
Simone Caligola
,
Luca Giacobazzi
,
Stefania Canè
,
Antonio Vella
,
Annalisa Adamo
...
Data and text mining
TransGEM: a molecule generation model based on Transformer with gene expression data
Yanguang Liu
,
Hailong Yu
,
Xinya Duan
,
Xiaomin Zhang
,
Ting Cheng
...
From cell lines to cancer patients: personalized drug synergy prediction
Halil Ibrahim Kuru
,
A Ercument Cicek
,
Oznur Tastan
BTR: a bioinformatics tool recommendation system
Ryan Green
,
Xufeng Qu
,
Jinze Liu
,
Tingting Yu
Molecular property prediction based on graph structure learning
Bangyi Zhao
,
Weixia Xu
,
Jihong Guan
,
Shuigeng Zhou
Pathformer: a biological pathway informed transformer for disease diagnosis and prognosis using multi-omics data
Xiaofan Liu
,
Yuhuan Tao
,
Zilin Cai
,
Pengfei Bao
,
Hongli Ma
...
Databases and ontologies
Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning
Azza Althagafi
,
Fernando Zhapa-Camacho
,
Robert Hoehndorf
Bioimage informatics
Automated segmentation and recognition of
C. elegans
whole-body cells
Yuanyuan Li
,
Chuxiao Lai
,
Meng Wang
,
Jun Wu
,
Yongbin Li
...
Applications Note
Genome analysis
MammalMethylClock R package: software for DNA methylation-based epigenetic clocks in mammals
Joseph Zoller
,
Steve Horvath
methscore: a comprehensive R function for DNA methylation-based health predictors
Zongli Xu
,
Liang Niu
,
Jacob K Kresovich
,
Jack A Taylor
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
Bryce Kille
,
Michael G Nute
,
Victor Huang
,
Eddie Kim
,
Adam M Phillippy
...
Sequence analysis
SimReadUntil for benchmarking selective sequencing algorithms on ONT devices
Maximilian Mordig
,
Gunnar Rätsch
,
André Kahles
Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper
Charlotte Crauwels
,
Sophie-Luise Heidig
,
Adrián Díaz
,
Wim F Vranken
PlasCAT: Plasmid Cloud Assembly Tool
Samuel Peccoud
,
Casey-Tyler Berezin
,
Sarah I Hernandez
,
Jean Peccoud
PQSDC: a parallel lossless compressor for quality scores data via sequences partition and run-length prediction mapping
Hui Sun
,
Yingfeng Zheng
,
Haonan Xie
,
Huidong Ma
,
Cheng Zhong
...
Phylogenetics
pipesnake
: generalized software for the assembly and analysis of phylogenomic datasets from conserved genomic loci
Ian G Brennan
,
Sonal Singhal
,
Ziad Al Bkhetan
Structural bioinformatics
CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences
Nikolaos Louros
,
Frederic Rousseau
,
Joost Schymkowitz
Peptriever: a Bi-Encoder approach for large-scale protein'peptide binding search
Roni Gurvich
,
Gal Markel
,
Ziaurrehman Tanoli
,
Tomer Meirson
Gene expression
CASCC: a co-expression-assisted single-cell RNA-seq data clustering method
Lingyi Cai
,
Dimitris Anastassiou
greenPipes: an integrated data analysis pipeline for greenCUT&RUN and CUT&RUN genome-localization datasets
Sheikh Nizamuddin
,
H T Marc Timmers
MultiRNAflow: integrated analysis of temporal RNA-seq data with multiple biological conditions
Rodolphe Loubaton
,
Nicolas Champagnat
,
Pierre Vallois
,
Laurent Vallat
Genetics and population analysis
shinyseg: a web application for flexible cosegregation and sensitivity analysis
Christian Carrizosa
,
Dag E Undlien
,
Magnus D Vigeland
MPH: fast REML for large-scale genome partitioning of quantitative genetic variation
Jicai Jiang
metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia
Zulema Rodriguez-Hernandez
,
Mathias Gorski
,
Maria Tellez-Plaza
,
Pascal Schlosser
,
Matthias Wuttke
Systems biology
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
Johanna Galvis
,
Joris Guyon
,
Benjamin Dartigues
,
Helge Hecht
,
Björn Grüning
...
Data and text mining
NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph
Antonio Di Maria
,
Lorenzo Bellomo
,
Fabrizio Billeci
,
Alfio Cardillo
,
Salvatore Alaimo
...
ITree
: a user-driven tool for interactive decision-making with classification trees
Hubert Sokołowski
,
Marcin Czajkowski
,
Anna Czajkowska
,
Krzysztof Jurczuk
,
Marek Kretowski
Correction
Correction to: kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase
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